HEADER DNA BINDING PROTEIN/DNA 19-APR-12 4ER8 TITLE STRUCTURE OF THE REP ASSOCIATES TYROSINE TRANSPOSASE BOUND TO A REP TITLE 2 HAIRPIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: TNPAREP FOR PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: UNCHARACTERIZED PROTEIN YAFM; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DNA (32-MER); COMPND 8 CHAIN: B; COMPND 9 ENGINEERED: YES; COMPND 10 OTHER_DETAILS: REPETATIVE EXTRAGENIC PALINDROMIC SEQUENCE FOR DNA SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: MG1655; SOURCE 5 GENE: B0228, JW0218, TNPAREP, YAFM; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: TOP10; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PBAD; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES KEYWDS PROTEIN-DNA COMPLEX, GUIDE SEQUENCE, CATALYTIC TYROSINE, RNA KEYWDS 2 RECOGNITION MOTIF, TRANSPOSASE, HUH MOTIF, DNA BINDING PROTEIN-DNA KEYWDS 3 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR S.A.J.MESSING,B.TON-HOANG,A.B.HICKMAN,R.GHIRLANDO,M.CHANDLER,F.DYDA REVDAT 4 28-FEB-24 4ER8 1 REMARK LINK REVDAT 3 02-JAN-13 4ER8 1 JRNL REVDAT 2 29-AUG-12 4ER8 1 JRNL REVDAT 1 15-AUG-12 4ER8 0 JRNL AUTH S.A.MESSING,B.TON-HOANG,A.B.HICKMAN,A.J.MCCUBBIN, JRNL AUTH 2 G.F.PEASLEE,R.GHIRLANDO,M.CHANDLER,F.DYDA JRNL TITL THE PROCESSING OF REPETITIVE EXTRAGENIC PALINDROMES: THE JRNL TITL 2 STRUCTURE OF A REPETITIVE EXTRAGENIC PALINDROME BOUND TO ITS JRNL TITL 3 ASSOCIATED NUCLEASE. JRNL REF NUCLEIC ACIDS RES. V. 40 9964 2012 JRNL REFN ISSN 0305-1048 JRNL PMID 22885300 JRNL DOI 10.1093/NAR/GKS741 REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.26 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 92.0 REMARK 3 NUMBER OF REFLECTIONS : 12056 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) : 0.228 REMARK 3 R VALUE (WORKING SET) : 0.225 REMARK 3 FREE R VALUE : 0.281 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 635 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) : 2.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.67 REMARK 3 REFLECTION IN BIN (WORKING SET) : 760 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 79.74 REMARK 3 BIN R VALUE (WORKING SET) : 0.3430 REMARK 3 BIN FREE R VALUE SET COUNT : 35 REMARK 3 BIN FREE R VALUE : 0.4060 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1422 REMARK 3 NUCLEIC ACID ATOMS : 658 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 22 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 54.11 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.39000 REMARK 3 B22 (A**2) : -1.59000 REMARK 3 B33 (A**2) : -1.80000 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): 0.465 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.320 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.233 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 10.734 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.934 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.895 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2211 ; 0.016 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3137 ; 1.930 ; 2.294 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 164 ; 6.620 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 81 ;33.407 ;21.728 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 242 ;19.805 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 16 ;21.073 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 324 ; 0.102 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1496 ; 0.009 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): 823 ; 0.900 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1339 ; 1.753 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1388 ; 2.036 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1798 ; 3.170 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 4ER8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-APR-12. REMARK 100 THE DEPOSITION ID IS D_1000071969. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-JUL-11 REMARK 200 TEMPERATURE (KELVIN) : 95 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : MULTILAYER FOCUSING OPTICS REMARK 200 OPTICS : MULTILAYER FOCUSING OPTICS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25580 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 23.500 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.04000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 23.4600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.67 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.56500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.230 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 65.72 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.59 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 5000 MME, MES, 1-PROPANOL, PH 6.5, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K 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 50.41500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.15000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 50.41500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 30.15000 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: 2950 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12940 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -13.0 KCAL/MOL 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 NH2 ARG A 21 OP2 DG B 5 2.14 REMARK 500 OD1 ASP A 70 NH2 ARG A 76 2.15 REMARK 500 REMARK 500 REMARK: NULL 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 DT B 2 O3' DT B 2 C3' -0.042 REMARK 500 DA B 3 O3' DA B 3 C3' -0.047 REMARK 500 DA B 10 O3' DA B 10 C3' -0.039 REMARK 500 DC B 27 O3' DC B 27 C3' -0.086 REMARK 500 DC B 31 O3' DC B 31 C3' -0.060 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 ASP A 114 CB - CG - OD1 ANGL. DEV. = 5.6 DEGREES REMARK 500 DG B 1 O4' - C1' - N9 ANGL. DEV. = -6.3 DEGREES REMARK 500 DT B 2 O5' - C5' - C4' ANGL. DEV. = -5.1 DEGREES REMARK 500 DT B 2 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 DA B 3 O5' - P - OP1 ANGL. DEV. = 7.9 DEGREES REMARK 500 DA B 3 O4' - C1' - N9 ANGL. DEV. = -5.3 DEGREES REMARK 500 DG B 5 O4' - C1' - N9 ANGL. DEV. = -5.2 DEGREES REMARK 500 DC B 7 C3' - O3' - P ANGL. DEV. = 10.0 DEGREES REMARK 500 DG B 9 C3' - C2' - C1' ANGL. DEV. = -5.7 DEGREES REMARK 500 DA B 12 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DG B 14 O4' - C1' - N9 ANGL. DEV. = 6.0 DEGREES REMARK 500 DG B 15 O4' - C1' - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 DC B 16 O4' - C4' - C3' ANGL. DEV. = -2.9 DEGREES REMARK 500 DC B 16 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 DG B 17 O4' - C4' - C3' ANGL. DEV. = -4.3 DEGREES REMARK 500 DG B 17 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 DT B 18 O4' - C1' - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 DT B 18 C4 - C5 - C7 ANGL. DEV. = 3.6 DEGREES REMARK 500 DT B 19 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 DA B 21 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 DC B 22 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 DG B 23 O4' - C1' - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 DG B 23 C8 - N9 - C4 ANGL. DEV. = -2.4 DEGREES REMARK 500 DG B 26 O4' - C1' - N9 ANGL. DEV. = 8.9 DEGREES REMARK 500 DT B 29 C5 - C4 - O4 ANGL. DEV. = -4.9 DEGREES REMARK 500 DC B 31 O4' - C1' - N1 ANGL. DEV. = -5.4 DEGREES REMARK 500 DC B 31 N3 - C4 - C5 ANGL. DEV. = -2.8 DEGREES REMARK 500 DC B 31 N3 - C2 - O2 ANGL. DEV. = 4.7 DEGREES REMARK 500 DC B 31 N3 - C4 - N4 ANGL. DEV. = 4.5 DEGREES REMARK 500 DC B 31 C3' - O3' - P ANGL. DEV. = 10.4 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 THR A 29 -60.69 -91.66 REMARK 500 GLN A 31 36.13 -96.17 REMARK 500 PRO A 67 161.47 -46.82 REMARK 500 ARG A 97 -139.56 40.15 REMARK 500 PHE A 134 59.06 -90.67 REMARK 500 ALA A 159 18.85 -157.24 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ALA A 142 ARG A 143 149.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI A 201 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 59 NE2 REMARK 620 2 HIS A 61 NE2 89.3 REMARK 620 3 ASN A 119 OD1 111.9 84.5 REMARK 620 4 HIS A 123 NE2 92.3 173.6 89.2 REMARK 620 5 GLU A 161 OE2 141.3 85.7 105.7 96.8 REMARK 620 6 GLU A 161 OE1 82.1 91.0 165.1 95.3 59.7 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A 201 DBREF 4ER8 A 1 165 UNP Q47152 YAFM_ECOLI 1 165 DBREF 4ER8 B 1 32 PDB 4ER8 4ER8 1 32 SEQRES 1 A 165 MET SER GLU TYR ARG ARG TYR TYR ILE LYS GLY GLY THR SEQRES 2 A 165 TRP PHE PHE THR VAL ASN LEU ARG ASN ARG ARG SER GLN SEQRES 3 A 165 LEU LEU THR THR GLN TYR GLN MET LEU ARG HIS ALA ILE SEQRES 4 A 165 ILE LYS VAL LYS ARG ASP ARG PRO PHE GLU ILE ASN ALA SEQRES 5 A 165 TRP VAL VAL LEU PRO GLU HIS MET HIS CYS ILE TRP THR SEQRES 6 A 165 LEU PRO GLU GLY ASP ASP ASP PHE SER SER ARG TRP ARG SEQRES 7 A 165 GLU ILE LYS LYS GLN PHE THR HIS ALA CYS GLY LEU LYS SEQRES 8 A 165 ASN ILE TRP GLN PRO ARG PHE TRP GLU HIS ALA ILE ARG SEQRES 9 A 165 ASN THR LYS ASP TYR ARG HIS HIS VAL ASP TYR ILE TYR SEQRES 10 A 165 ILE ASN PRO VAL LYS HIS GLY TRP VAL LYS GLN VAL SER SEQRES 11 A 165 ASP TRP PRO PHE SER THR PHE HIS ARG ASP VAL ALA ARG SEQRES 12 A 165 GLY LEU TYR PRO ILE ASP TRP ALA GLY ASP VAL THR ASP SEQRES 13 A 165 PHE SER ALA GLY GLU ARG ILE ILE SER SEQRES 1 B 32 DG DT DA DG DG DA DC DG DG DA DT DA DA SEQRES 2 B 32 DG DG DC DG DT DT DT DA DC DG DC DC DG SEQRES 3 B 32 DC DA DT DC DC DG HET NI A 201 1 HETNAM NI NICKEL (II) ION FORMUL 3 NI NI 2+ FORMUL 4 HOH *22(H2 O) HELIX 1 1 GLN A 26 GLN A 31 1 6 HELIX 2 2 GLN A 31 ARG A 46 1 16 HELIX 3 3 ASP A 72 CYS A 88 1 17 HELIX 4 4 ASN A 105 HIS A 123 1 19 HELIX 5 5 GLN A 128 TRP A 132 5 5 HELIX 6 6 THR A 136 ARG A 143 1 8 SHEET 1 A 4 GLU A 49 VAL A 55 0 SHEET 2 A 4 HIS A 59 THR A 65 -1 O ILE A 63 N ALA A 52 SHEET 3 A 4 THR A 13 ASN A 19 -1 N VAL A 18 O MET A 60 SHEET 4 A 4 TRP A 99 ALA A 102 -1 O HIS A 101 N PHE A 15 LINK NE2 HIS A 59 NI NI A 201 1555 1555 2.09 LINK NE2 HIS A 61 NI NI A 201 1555 1555 2.00 LINK OD1 ASN A 119 NI NI A 201 1555 1555 2.16 LINK NE2 HIS A 123 NI NI A 201 1555 1555 2.03 LINK OE2 GLU A 161 NI NI A 201 1555 1555 2.10 LINK OE1 GLU A 161 NI NI A 201 1555 1555 2.28 SITE 1 AC1 5 HIS A 59 HIS A 61 ASN A 119 HIS A 123 SITE 2 AC1 5 GLU A 161 CRYST1 100.830 60.300 70.780 90.00 90.00 90.00 P 21 21 2 4 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 0.009918 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016584 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014128 0.00000