HEADER LYASE 08-NOV-07 3BAR TITLE CRYSTAL STRUCTURE OF PLASMODIUM FALCIPARUM OROTIDINE 5'-PHOSPHATE TITLE 2 DECARBOXYLASE COVALENTLY MODIFIED BY 6-AZIDO-UMP COMPND MOL_ID: 1; COMPND 2 MOLECULE: OROTIDINE 5'-PHOSPHATE DECARBOXYLASE; COMPND 3 CHAIN: A, B; COMPND 4 EC: 4.1.1.23; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PLASMODIUM FALCIPARUM; SOURCE 3 ORGANISM_TAXID: 36329; SOURCE 4 STRAIN: 3D7; SOURCE 5 GENE: OMPDC; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21-RIL(DE23); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28A-LIC KEYWDS PLASMODIUM FALCIPARUM, OROTIDINE 5'-PHOSPHATE DECARBOXYLASE, KEYWDS 2 COVALENTLY, 6-AZIDO-UMP, LYASE, PYRIMIDINE BIOSYNTHESIS EXPDTA X-RAY DIFFRACTION AUTHOR Y.LIU,A.M.BELLO,E.PODUCH,W.LAU,L.P.KOTRA,E.F.PAI REVDAT 4 13-JUL-11 3BAR 1 VERSN REVDAT 3 24-FEB-09 3BAR 1 VERSN REVDAT 2 19-FEB-08 3BAR 1 JRNL REVDAT 1 29-JAN-08 3BAR 0 JRNL AUTH A.M.BELLO,E.PODUCH,Y.LIU,L.WEI,I.CRANDALL,X.WANG,C.DYANAND, JRNL AUTH 2 K.C.KAIN,E.F.PAI,L.P.KOTRA JRNL TITL STRUCTURE-ACTIVITY RELATIONSHIPS OF C6-URIDINE DERIVATIVES JRNL TITL 2 TARGETING PLASMODIA OROTIDINE MONOPHOSPHATE DECARBOXYLASE. JRNL REF J.MED.CHEM. V. 51 439 2008 JRNL REFN ISSN 0022-2623 JRNL PMID 18189347 JRNL DOI 10.1021/JM7010673 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.68 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.4 REMARK 3 NUMBER OF REFLECTIONS : 44155 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.174 REMARK 3 R VALUE (WORKING SET) : 0.172 REMARK 3 FREE R VALUE : 0.219 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2357 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.95 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3250 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.45 REMARK 3 BIN R VALUE (WORKING SET) : 0.1960 REMARK 3 BIN FREE R VALUE SET COUNT : 167 REMARK 3 BIN FREE R VALUE : 0.2540 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5308 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 42 REMARK 3 SOLVENT ATOMS : 256 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.07 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.49000 REMARK 3 B22 (A**2) : -0.19000 REMARK 3 B33 (A**2) : -0.31000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.173 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.154 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.097 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.192 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.958 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.938 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5534 ; 0.010 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7477 ; 1.518 ; 1.965 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 655 ; 5.871 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 287 ;39.745 ;25.819 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1007 ;14.035 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 12 ;24.013 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 797 ; 0.107 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4206 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2779 ; 0.228 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 3945 ; 0.316 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 330 ; 0.149 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 48 ; 0.222 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 11 ; 0.146 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 3350 ; 1.017 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5288 ; 1.613 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2498 ; 2.530 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2189 ; 3.725 ; 4.500 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: PROGRAM COOT 0.1.3-PRE-1 HAS ALSO BEEN REMARK 3 USED IN REFINEMENT REMARK 4 REMARK 4 3BAR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-NOV-07. REMARK 100 THE RCSB ID CODE IS RCSB045291. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-AUG-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 9.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CLSI REMARK 200 BEAMLINE : 08ID-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97934 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : DCM WITH CRYO-COOLED 1ST CRYSTAL REMARK 200 SAGITALLY BENT 2ND CRYSTAL REMARK 200 FOLLOWED BY VERTICALLY FOCUSING REMARK 200 MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 44155 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.4 REMARK 200 DATA REDUNDANCY : 5.200 REMARK 200 R MERGE (I) : 0.08500 REMARK 200 R SYM (I) : 0.08500 REMARK 200 FOR THE DATA SET : 11.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.9 REMARK 200 DATA REDUNDANCY IN SHELL : 5.10 REMARK 200 R MERGE FOR SHELL (I) : 0.45900 REMARK 200 R SYM FOR SHELL (I) : 0.45900 REMARK 200 FOR SHELL : 3.450 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 2Q8L REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.24 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM AMMONIUM PHOSPHATE, 27% PEG REMARK 280 1000, PH 9.2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 40.46400 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 41.67700 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 40.46400 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 41.67700 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4700 ANGSTROM**2 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A3036 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A -18 REMARK 465 GLY A -17 REMARK 465 SER A -16 REMARK 465 SER A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 HIS A -9 REMARK 465 SER A -8 REMARK 465 SER A -7 REMARK 465 GLY A -6 REMARK 465 LEU A -5 REMARK 465 VAL A -4 REMARK 465 PRO A -3 REMARK 465 ARG A -2 REMARK 465 GLU A 322 REMARK 465 SER A 323 REMARK 465 MET B -18 REMARK 465 GLY B -17 REMARK 465 SER B -16 REMARK 465 SER B -15 REMARK 465 HIS B -14 REMARK 465 HIS B -13 REMARK 465 HIS B -12 REMARK 465 HIS B -11 REMARK 465 HIS B -10 REMARK 465 HIS B -9 REMARK 465 SER B -8 REMARK 465 SER B -7 REMARK 465 GLY B -6 REMARK 465 LEU B -5 REMARK 465 VAL B -4 REMARK 465 PRO B -3 REMARK 465 ARG B -2 REMARK 465 GLY B -1 REMARK 465 GLU B 322 REMARK 465 SER B 323 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 MET A 137 C LYS A 138 N 0.165 REMARK 500 LYS A 138 C ILE A 139 N 0.200 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 LYS A 138 CD - CE - NZ ANGL. DEV. = 14.2 DEGREES REMARK 500 LYS B 138 CD - CE - NZ ANGL. DEV. = 20.5 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 SER A 0 59.45 -104.80 REMARK 500 ASP A 209 -126.63 57.58 REMARK 500 SER A 245 60.91 -110.25 REMARK 500 ASP B 209 -130.44 59.12 REMARK 500 SER B 245 71.06 -114.46 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 ASN B 210 22.2 L L OUTSIDE RANGE REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH B3123 DISTANCE = 5.05 ANGSTROMS REMARK 525 HOH B3126 DISTANCE = 5.32 ANGSTROMS REMARK 600 REMARK 600 HETEROGEN REMARK 600 THERE IS A COVALENT BOND FORMED BETWEEN CARBON-6 REMARK 600 OF THE URIDINE RING OF UMP AND THE NZ-NITROGEN REMARK 600 OF LYS138 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE U5P A 3000 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE U5P B 3000 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2Q8L RELATED DB: PDB REMARK 900 APO STRUCTURE OF OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE REMARK 900 FROM PLASMODIUM FALCIPARUM REMARK 900 RELATED ID: 2Q8Z RELATED DB: PDB REMARK 900 STRUCTURE OF PLASMODIUM FALCIPARUM OROTIDINE 5'-PHOSPHATE REMARK 900 DECARBOXYLASE COMPLEXED WITH 6-AMINO-UMP REMARK 900 RELATED ID: 2QAF RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF PLASMODIUM FALCIPARUM OROTIDINE 5'- REMARK 900 PHOSPHATE DECARBOXYLASE COVALENTLY MODIFIED BY 6-IODO-UMP DBREF 3BAR A 1 323 UNP Q8T6J6 Q8T6J6_PLAFA 1 323 DBREF 3BAR B 1 323 UNP Q8T6J6 Q8T6J6_PLAFA 1 323 SEQADV 3BAR MET A -18 UNP Q8T6J6 EXPRESSION TAG SEQADV 3BAR GLY A -17 UNP Q8T6J6 EXPRESSION TAG SEQADV 3BAR SER A -16 UNP Q8T6J6 EXPRESSION TAG SEQADV 3BAR SER A -15 UNP Q8T6J6 EXPRESSION TAG SEQADV 3BAR HIS A -14 UNP Q8T6J6 EXPRESSION TAG SEQADV 3BAR HIS A -13 UNP Q8T6J6 EXPRESSION TAG SEQADV 3BAR HIS A -12 UNP Q8T6J6 EXPRESSION TAG SEQADV 3BAR HIS A -11 UNP Q8T6J6 EXPRESSION TAG SEQADV 3BAR HIS A -10 UNP Q8T6J6 EXPRESSION TAG SEQADV 3BAR HIS A -9 UNP Q8T6J6 EXPRESSION TAG SEQADV 3BAR SER A -8 UNP Q8T6J6 EXPRESSION TAG SEQADV 3BAR SER A -7 UNP Q8T6J6 EXPRESSION TAG SEQADV 3BAR GLY A -6 UNP Q8T6J6 EXPRESSION TAG SEQADV 3BAR LEU A -5 UNP Q8T6J6 EXPRESSION TAG SEQADV 3BAR VAL A -4 UNP Q8T6J6 EXPRESSION TAG SEQADV 3BAR PRO A -3 UNP Q8T6J6 EXPRESSION TAG SEQADV 3BAR ARG A -2 UNP Q8T6J6 EXPRESSION TAG SEQADV 3BAR GLY A -1 UNP Q8T6J6 EXPRESSION TAG SEQADV 3BAR SER A 0 UNP Q8T6J6 EXPRESSION TAG SEQADV 3BAR MET B -18 UNP Q8T6J6 EXPRESSION TAG SEQADV 3BAR GLY B -17 UNP Q8T6J6 EXPRESSION TAG SEQADV 3BAR SER B -16 UNP Q8T6J6 EXPRESSION TAG SEQADV 3BAR SER B -15 UNP Q8T6J6 EXPRESSION TAG SEQADV 3BAR HIS B -14 UNP Q8T6J6 EXPRESSION TAG SEQADV 3BAR HIS B -13 UNP Q8T6J6 EXPRESSION TAG SEQADV 3BAR HIS B -12 UNP Q8T6J6 EXPRESSION TAG SEQADV 3BAR HIS B -11 UNP Q8T6J6 EXPRESSION TAG SEQADV 3BAR HIS B -10 UNP Q8T6J6 EXPRESSION TAG SEQADV 3BAR HIS B -9 UNP Q8T6J6 EXPRESSION TAG SEQADV 3BAR SER B -8 UNP Q8T6J6 EXPRESSION TAG SEQADV 3BAR SER B -7 UNP Q8T6J6 EXPRESSION TAG SEQADV 3BAR GLY B -6 UNP Q8T6J6 EXPRESSION TAG SEQADV 3BAR LEU B -5 UNP Q8T6J6 EXPRESSION TAG SEQADV 3BAR VAL B -4 UNP Q8T6J6 EXPRESSION TAG SEQADV 3BAR PRO B -3 UNP Q8T6J6 EXPRESSION TAG SEQADV 3BAR ARG B -2 UNP Q8T6J6 EXPRESSION TAG SEQADV 3BAR GLY B -1 UNP Q8T6J6 EXPRESSION TAG SEQADV 3BAR SER B 0 UNP Q8T6J6 EXPRESSION TAG SEQRES 1 A 342 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 342 LEU VAL PRO ARG GLY SER MET GLY PHE LYS VAL LYS LEU SEQRES 3 A 342 GLU LYS ARG ARG ASN ALA ILE ASN THR CYS LEU CYS ILE SEQRES 4 A 342 GLY LEU ASP PRO ASP GLU LYS ASP ILE GLU ASN PHE MET SEQRES 5 A 342 LYS ASN GLU LYS GLU ASN ASN TYR ASN ASN ILE LYS LYS SEQRES 6 A 342 ASN LEU LYS GLU LYS TYR ILE ASN ASN VAL SER ILE LYS SEQRES 7 A 342 LYS ASP ILE LEU LEU LYS ALA PRO ASP ASN ILE ILE ARG SEQRES 8 A 342 GLU GLU LYS SER GLU GLU PHE PHE TYR PHE PHE ASN HIS SEQRES 9 A 342 PHE CYS PHE TYR ILE ILE ASN GLU THR ASN LYS TYR ALA SEQRES 10 A 342 LEU THR PHE LYS MET ASN PHE ALA PHE TYR ILE PRO TYR SEQRES 11 A 342 GLY SER VAL GLY ILE ASP VAL LEU LYS ASN VAL PHE ASP SEQRES 12 A 342 TYR LEU TYR GLU LEU ASN ILE PRO THR ILE LEU ASP MET SEQRES 13 A 342 LYS ILE ASN ASP ILE GLY ASN THR VAL LYS ASN TYR ARG SEQRES 14 A 342 LYS PHE ILE PHE GLU TYR LEU LYS SER ASP SER CYS THR SEQRES 15 A 342 VAL ASN ILE TYR MET GLY THR ASN MET LEU LYS ASP ILE SEQRES 16 A 342 CYS TYR ASP GLU GLU LYS ASN LYS TYR TYR SER ALA PHE SEQRES 17 A 342 VAL LEU VAL LYS THR THR ASN PRO ASP SER ALA ILE PHE SEQRES 18 A 342 GLN LYS ASN LEU SER LEU ASP ASN LYS GLN ALA TYR VAL SEQRES 19 A 342 ILE MET ALA GLN GLU ALA LEU ASN MET SER SER TYR LEU SEQRES 20 A 342 ASN LEU GLU GLN ASN ASN GLU PHE ILE GLY PHE VAL VAL SEQRES 21 A 342 GLY ALA ASN SER TYR ASP GLU MET ASN TYR ILE ARG THR SEQRES 22 A 342 TYR PHE PRO ASN CYS TYR ILE LEU SER PRO GLY ILE GLY SEQRES 23 A 342 ALA GLN ASN GLY ASP LEU HIS LYS THR LEU THR ASN GLY SEQRES 24 A 342 TYR HIS LYS SER TYR GLU LYS ILE LEU ILE ASN ILE GLY SEQRES 25 A 342 ARG ALA ILE THR LYS ASN PRO TYR PRO GLN LYS ALA ALA SEQRES 26 A 342 GLN MET TYR TYR ASP GLN ILE ASN ALA ILE LEU LYS GLN SEQRES 27 A 342 ASN MET GLU SER SEQRES 1 B 342 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 B 342 LEU VAL PRO ARG GLY SER MET GLY PHE LYS VAL LYS LEU SEQRES 3 B 342 GLU LYS ARG ARG ASN ALA ILE ASN THR CYS LEU CYS ILE SEQRES 4 B 342 GLY LEU ASP PRO ASP GLU LYS ASP ILE GLU ASN PHE MET SEQRES 5 B 342 LYS ASN GLU LYS GLU ASN ASN TYR ASN ASN ILE LYS LYS SEQRES 6 B 342 ASN LEU LYS GLU LYS TYR ILE ASN ASN VAL SER ILE LYS SEQRES 7 B 342 LYS ASP ILE LEU LEU LYS ALA PRO ASP ASN ILE ILE ARG SEQRES 8 B 342 GLU GLU LYS SER GLU GLU PHE PHE TYR PHE PHE ASN HIS SEQRES 9 B 342 PHE CYS PHE TYR ILE ILE ASN GLU THR ASN LYS TYR ALA SEQRES 10 B 342 LEU THR PHE LYS MET ASN PHE ALA PHE TYR ILE PRO TYR SEQRES 11 B 342 GLY SER VAL GLY ILE ASP VAL LEU LYS ASN VAL PHE ASP SEQRES 12 B 342 TYR LEU TYR GLU LEU ASN ILE PRO THR ILE LEU ASP MET SEQRES 13 B 342 LYS ILE ASN ASP ILE GLY ASN THR VAL LYS ASN TYR ARG SEQRES 14 B 342 LYS PHE ILE PHE GLU TYR LEU LYS SER ASP SER CYS THR SEQRES 15 B 342 VAL ASN ILE TYR MET GLY THR ASN MET LEU LYS ASP ILE SEQRES 16 B 342 CYS TYR ASP GLU GLU LYS ASN LYS TYR TYR SER ALA PHE SEQRES 17 B 342 VAL LEU VAL LYS THR THR ASN PRO ASP SER ALA ILE PHE SEQRES 18 B 342 GLN LYS ASN LEU SER LEU ASP ASN LYS GLN ALA TYR VAL SEQRES 19 B 342 ILE MET ALA GLN GLU ALA LEU ASN MET SER SER TYR LEU SEQRES 20 B 342 ASN LEU GLU GLN ASN ASN GLU PHE ILE GLY PHE VAL VAL SEQRES 21 B 342 GLY ALA ASN SER TYR ASP GLU MET ASN TYR ILE ARG THR SEQRES 22 B 342 TYR PHE PRO ASN CYS TYR ILE LEU SER PRO GLY ILE GLY SEQRES 23 B 342 ALA GLN ASN GLY ASP LEU HIS LYS THR LEU THR ASN GLY SEQRES 24 B 342 TYR HIS LYS SER TYR GLU LYS ILE LEU ILE ASN ILE GLY SEQRES 25 B 342 ARG ALA ILE THR LYS ASN PRO TYR PRO GLN LYS ALA ALA SEQRES 26 B 342 GLN MET TYR TYR ASP GLN ILE ASN ALA ILE LEU LYS GLN SEQRES 27 B 342 ASN MET GLU SER HET U5P A3000 21 HET U5P B3000 21 HETNAM U5P URIDINE-5'-MONOPHOSPHATE FORMUL 3 U5P 2(C9 H13 N2 O9 P) FORMUL 5 HOH *256(H2 O) HELIX 1 1 GLY A 2 ASN A 15 1 14 HELIX 2 2 ASP A 25 ASN A 39 1 15 HELIX 3 3 TYR A 41 GLU A 50 1 10 HELIX 4 4 LYS A 51 VAL A 56 5 6 HELIX 5 5 LYS A 59 LEU A 64 1 6 HELIX 6 6 ALA A 66 GLU A 74 1 9 HELIX 7 7 GLU A 77 ASN A 95 1 19 HELIX 8 8 LYS A 96 ALA A 98 5 3 HELIX 9 9 ALA A 106 TYR A 108 5 3 HELIX 10 10 GLY A 112 ASN A 130 1 19 HELIX 11 11 ILE A 142 GLU A 155 1 14 HELIX 12 12 THR A 170 ILE A 176 5 7 HELIX 13 13 SER A 199 LYS A 204 1 6 HELIX 14 14 ALA A 213 LEU A 228 1 16 HELIX 15 15 LEU A 230 ASN A 234 5 5 HELIX 16 16 SER A 245 PHE A 256 1 12 HELIX 17 17 ASP A 272 TYR A 281 1 10 HELIX 18 18 SER A 284 GLU A 286 5 3 HELIX 19 19 GLY A 293 LYS A 298 1 6 HELIX 20 20 TYR A 301 MET A 321 1 21 HELIX 21 21 GLY B 2 ASN B 15 1 14 HELIX 22 22 ASP B 25 ASN B 39 1 15 HELIX 23 23 TYR B 41 LYS B 49 1 9 HELIX 24 24 GLU B 50 VAL B 56 5 7 HELIX 25 25 LYS B 59 LYS B 65 1 7 HELIX 26 26 ALA B 66 GLU B 74 1 9 HELIX 27 27 GLU B 77 ASN B 95 1 19 HELIX 28 28 LYS B 96 ALA B 98 5 3 HELIX 29 29 ALA B 106 TYR B 108 5 3 HELIX 30 30 SER B 113 LEU B 129 1 17 HELIX 31 31 ILE B 142 GLU B 155 1 14 HELIX 32 32 THR B 170 ILE B 176 5 7 HELIX 33 33 SER B 199 LYS B 204 1 6 HELIX 34 34 ALA B 213 LEU B 228 1 16 HELIX 35 35 LEU B 230 ASN B 234 5 5 HELIX 36 36 SER B 245 PHE B 256 1 12 HELIX 37 37 ASP B 272 GLY B 280 1 9 HELIX 38 38 SER B 284 GLU B 286 5 3 HELIX 39 39 GLY B 293 LYS B 298 1 6 HELIX 40 40 TYR B 301 ASN B 320 1 20 SHEET 1 A 9 LEU A 18 GLY A 21 0 SHEET 2 A 9 THR A 100 ASN A 104 1 O THR A 100 N ILE A 20 SHEET 3 A 9 THR A 133 ILE A 139 1 O ASP A 136 N MET A 103 SHEET 4 A 9 SER A 161 VAL A 164 1 O SER A 161 N LEU A 135 SHEET 5 A 9 SER A 187 LYS A 193 1 O PHE A 189 N CYS A 162 SHEET 6 A 9 ILE A 237 VAL A 241 1 O VAL A 240 N VAL A 190 SHEET 7 A 9 ILE A 261 SER A 263 1 O LEU A 262 N PHE A 239 SHEET 8 A 9 ILE A 288 ILE A 292 1 O LEU A 289 N SER A 263 SHEET 9 A 9 LEU A 18 GLY A 21 1 N CYS A 19 O ILE A 290 SHEET 1 B 2 TYR A 178 ASP A 179 0 SHEET 2 B 2 LYS A 184 TYR A 185 -1 O LYS A 184 N ASP A 179 SHEET 1 C 2 SER A 207 LEU A 208 0 SHEET 2 C 2 LYS A 211 GLN A 212 -1 O LYS A 211 N LEU A 208 SHEET 1 D 9 LEU B 18 LEU B 22 0 SHEET 2 D 9 THR B 100 ASN B 104 1 O LYS B 102 N LEU B 22 SHEET 3 D 9 THR B 133 ILE B 139 1 O ASP B 136 N MET B 103 SHEET 4 D 9 SER B 161 VAL B 164 1 O SER B 161 N LEU B 135 SHEET 5 D 9 SER B 187 LYS B 193 1 O PHE B 189 N CYS B 162 SHEET 6 D 9 ILE B 237 VAL B 241 1 O VAL B 240 N VAL B 190 SHEET 7 D 9 ILE B 261 SER B 263 1 O LEU B 262 N PHE B 239 SHEET 8 D 9 ILE B 288 ILE B 292 1 O LEU B 289 N SER B 263 SHEET 9 D 9 LEU B 18 LEU B 22 1 N CYS B 19 O ILE B 290 SHEET 1 E 2 TYR B 178 ASP B 179 0 SHEET 2 E 2 LYS B 184 TYR B 185 -1 O LYS B 184 N ASP B 179 SHEET 1 F 2 SER B 207 LEU B 208 0 SHEET 2 F 2 LYS B 211 GLN B 212 -1 O LYS B 211 N LEU B 208 LINK NZ LYS A 138 C6 U5P A3000 1555 1555 1.37 LINK NZ LYS B 138 C6 U5P B3000 1555 1555 1.37 SITE 1 AC1 19 ASP A 23 LYS A 102 ASN A 104 ASP A 136 SITE 2 AC1 19 LYS A 138 THR A 194 THR A 195 PRO A 264 SITE 3 AC1 19 GLN A 269 GLY A 293 ARG A 294 HOH A3006 SITE 4 AC1 19 HOH A3007 HOH A3010 HOH A3011 HOH A3019 SITE 5 AC1 19 ASP B 141 ILE B 142 THR B 145 SITE 1 AC2 18 ASP A 141 THR A 145 ASP B 23 LYS B 102 SITE 2 AC2 18 ASN B 104 ASP B 136 LYS B 138 THR B 194 SITE 3 AC2 18 THR B 195 PRO B 264 GLN B 269 GLY B 293 SITE 4 AC2 18 ARG B 294 HOH B3002 HOH B3007 HOH B3010 SITE 5 AC2 18 HOH B3016 HOH B3022 CRYST1 80.928 83.354 89.872 90.00 90.00 90.00 P 21 21 2 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.012357 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011997 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011127 0.00000