HEADER TRANSCRIPTION 17-MAY-07 2V0R TITLE CRYSTAL STRUCTURE OF A HAIRPIN EXCHANGE VARIANT (LTX) OF TITLE 2 THE TARGETING LINE-1 RETROTRANSPOSON ENDONUCLEASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: LTX; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: RESIDUES 1-192,202-238; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PET KEYWDS APE-1 TYPE, ENDONUCLEASE, RETROTRANSPOSITION, RETROTRANSPOSON, KEYWDS 2 PROTEIN ENGINEERING, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR K.REPANAS,N.ZINGLER,L.E.LAYER,G.G.SCHUMANN,A.PERRAKIS, AUTHOR 2 O.WEICHENRIEDER REVDAT 4 13-JUL-11 2V0R 1 VERSN REVDAT 3 24-FEB-09 2V0R 1 VERSN REVDAT 2 21-AUG-07 2V0R 1 JRNL REVDAT 1 17-JUL-07 2V0R 0 JRNL AUTH K.REPANAS,N.ZINGLER,L.E.LAYER,G.G.SCHUMANN,A.PERRAKIS, JRNL AUTH 2 O.WEICHENRIEDER JRNL TITL DETERMINANTS FOR DNA TARGET STRUCTURE SELECTIVITY OF THE JRNL TITL 2 HUMAN LINE-1 RETROTRANSPOSON ENDONUCLEASE JRNL REF NUCLEIC ACIDS RES. V. 35 4914 2007 JRNL REFN ISSN 0305-1048 JRNL PMID 17626046 JRNL DOI 10.1093/NAR/GKM516 REMARK 2 REMARK 2 RESOLUTION. 2.3 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.53 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 21588 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) : 0.217 REMARK 3 R VALUE (WORKING SET) : 0.214 REMARK 3 FREE R VALUE : 0.272 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1156 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) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.36 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1502 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2560 REMARK 3 BIN FREE R VALUE SET COUNT : 79 REMARK 3 BIN FREE R VALUE : 0.3690 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3767 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 30 REMARK 3 SOLVENT ATOMS : 155 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.81 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.02000 REMARK 3 B22 (A**2) : -0.04000 REMARK 3 B33 (A**2) : 0.02000 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): 0.417 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.273 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.204 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 13.859 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.947 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.915 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3852 ; 0.020 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2673 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5197 ; 1.837 ; 1.965 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6545 ; 1.135 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 469 ;11.174 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 168 ;41.080 ;23.690 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 756 ;19.624 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 30 ;18.815 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 602 ; 0.113 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4132 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 726 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 757 ; 0.221 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 2796 ; 0.212 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1780 ; 0.171 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 2192 ; 0.093 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 160 ; 0.233 ; 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): 9 ; 0.265 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 29 ; 0.295 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 2 ; 0.288 ; 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): 3033 ; 1.478 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3810 ; 1.665 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1687 ; 2.187 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1386 ; 3.202 ; 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 : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 20 A 230 REMARK 3 ORIGIN FOR THE GROUP (A): 21.9894 26.9858 15.0030 REMARK 3 T TENSOR REMARK 3 T11: -0.1742 T22: -0.1382 REMARK 3 T33: -0.0489 T12: -0.0067 REMARK 3 T13: -0.0355 T23: -0.0040 REMARK 3 L TENSOR REMARK 3 L11: 1.3893 L22: 1.4229 REMARK 3 L33: 4.3741 L12: 0.0518 REMARK 3 L13: -0.5716 L23: -0.6803 REMARK 3 S TENSOR REMARK 3 S11: 0.0935 S12: -0.1445 S13: 0.0461 REMARK 3 S21: 0.1839 S22: -0.1114 S23: -0.0954 REMARK 3 S31: 0.0573 S32: 0.2121 S33: 0.0179 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 20 B 230 REMARK 3 ORIGIN FOR THE GROUP (A): 21.0730 43.4609 -15.1114 REMARK 3 T TENSOR REMARK 3 T11: -0.1078 T22: -0.1220 REMARK 3 T33: -0.0339 T12: -0.0275 REMARK 3 T13: 0.0131 T23: 0.0067 REMARK 3 L TENSOR REMARK 3 L11: 1.4991 L22: 1.0285 REMARK 3 L33: 7.4136 L12: -0.0559 REMARK 3 L13: 1.5179 L23: -0.7457 REMARK 3 S TENSOR REMARK 3 S11: -0.0373 S12: 0.2678 S13: -0.0059 REMARK 3 S21: -0.0248 S22: -0.0712 S23: -0.0858 REMARK 3 S31: -0.7486 S32: 0.4399 S33: 0.1084 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 REMARK 3 RIDING POSITIONS. REMARK 4 REMARK 4 2V0R COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 17-MAY-07. REMARK 100 THE PDBE ID CODE IS EBI-32590. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JUL-00 REMARK 200 TEMPERATURE (KELVIN) : 287 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.072 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22873 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.30 REMARK 200 RESOLUTION RANGE LOW (A) : 20.00 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.0 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 3 REMARK 200 R MERGE (I) : 0.11 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.80 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.3 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.4 REMARK 200 COMPLETENESS FOR SHELL (%) : 100 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.488 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.3 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 1VYB REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.06 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA):2.26 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 27.36300 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 65.11050 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.07100 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 65.11050 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.36300 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 35.07100 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 1 REMARK 465 THR A 2 REMARK 465 GLY A 3 REMARK 465 SER A 4 REMARK 465 ASN A 5 REMARK 465 MET B 1 REMARK 465 THR B 2 REMARK 465 GLY B 3 REMARK 465 SER B 4 REMARK 465 ASN B 5 REMARK 465 ARG B 240 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 CYS A 39 CB CYS A 39 SG -0.112 REMARK 500 CYS B 39 CB CYS B 39 SG -0.097 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 ARG A 197 NE - CZ - NH1 ANGL. DEV. = 3.1 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 LYS A 70 54.07 -90.13 REMARK 500 ALA A 72 -140.91 63.54 REMARK 500 GLN A 106 -11.38 82.42 REMARK 500 ASP A 137 -158.30 -149.03 REMARK 500 LYS A 220 -130.19 -85.21 REMARK 500 ALA B 72 -142.28 63.62 REMARK 500 GLN B 106 -10.02 79.85 REMARK 500 ASP B 137 -159.10 -153.89 REMARK 500 ARG B 158 18.06 58.89 REMARK 500 ASP B 176 51.30 37.44 REMARK 500 LYS B 220 -152.14 -78.69 REMARK 500 ARG B 221 112.94 -3.92 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 LYS B 220 ARG B 221 134.98 REMARK 500 ARG B 221 THR B 222 143.52 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 ARG A 221 22.7 L L OUTSIDE RANGE REMARK 500 ARG B 53 23.3 L L OUTSIDE RANGE REMARK 500 ASP B 176 24.7 L L OUTSIDE RANGE REMARK 500 LEU B 229 24.4 L L OUTSIDE RANGE REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A1241 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A1242 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A1243 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A1244 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B1240 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B1241 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1VYB RELATED DB: PDB REMARK 900 ENDONUCLEASE DOMAIN OF HUMAN LINE1 ORF2P REMARK 900 RELATED ID: 2V0S RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A HAIRPIN EXCHANGE REMARK 900 VARIANT (LR1) OF THE TARGETING LINE-1 REMARK 900 RETROTRANSPOSON ENDONUCLEASE REMARK 999 REMARK 999 SEQUENCE REMARK 999 THIS STRUCTURE IS A VARIANT OF THE PDB ENTRY 1VYB: L1 ENDONUCLEASE REMARK 999 DOMAIN. THE LOOP REGION 193-201 IS REPLACED WITH A LOOP BELONGING TO REMARK 999 RELATED ENDONUCLEASE. DBREF 2V0R A 1 192 UNP Q8TE30 Q8TE30_HUMAN 1 192 DBREF 2V0R A 193 203 PDB 2V0R 2V0R 193 203 DBREF 2V0R A 204 240 UNP Q8TE30 Q8TE30_HUMAN 202 238 DBREF 2V0R B 1 192 UNP Q8TE30 Q8TE30_HUMAN 1 192 DBREF 2V0R B 193 203 PDB 2V0R 2V0R 193 203 DBREF 2V0R B 204 240 UNP Q8TE30 Q8TE30_HUMAN 202 238 SEQRES 1 A 240 MET THR GLY SER ASN SER HIS ILE THR ILE LEU THR LEU SEQRES 2 A 240 ASN ILE ASN GLY LEU ASN SER ALA ILE LYS ARG HIS ARG SEQRES 3 A 240 LEU ALA SER TRP ILE LYS SER GLN ASP PRO SER VAL CYS SEQRES 4 A 240 CYS ILE GLN GLU THR HIS LEU THR CYS ARG ASP THR HIS SEQRES 5 A 240 ARG LEU LYS ILE LYS GLY TRP ARG LYS ILE TYR GLN ALA SEQRES 6 A 240 ASN GLY LYS GLN LYS LYS ALA GLY VAL ALA ILE LEU VAL SEQRES 7 A 240 SER ASP LYS THR ASP PHE LYS PRO THR LYS ILE LYS ARG SEQRES 8 A 240 ASP LYS GLU GLY HIS TYR ILE MET VAL LYS GLY SER ILE SEQRES 9 A 240 GLN GLN GLU GLU LEU THR ILE LEU ASN ILE TYR ALA PRO SEQRES 10 A 240 ASN THR GLY ALA PRO ARG PHE ILE LYS GLN VAL LEU SER SEQRES 11 A 240 ASP LEU GLN ARG ASP LEU ASP SER HIS THR LEU ILE MET SEQRES 12 A 240 GLY ASP PHE ASN THR PRO LEU SER THR LEU ASP ARG SER SEQRES 13 A 240 THR ARG GLN LYS VAL ASN LYS ASP THR GLN GLU LEU ASN SEQRES 14 A 240 SER ALA LEU HIS GLN ALA ASP LEU ILE ASP ILE TYR ARG SEQRES 15 A 240 THR LEU HIS PRO LYS SER THR GLU TYR THR TYR VAL ARG SEQRES 16 A 240 VAL ARG ASP GLY HIS VAL SER GLN SER LYS ILE ASP HIS SEQRES 17 A 240 ILE VAL GLY SER LYS ALA LEU LEU SER LYS CYS LYS ARG SEQRES 18 A 240 THR GLU ILE ILE THR ASN TYR LEU SER ASP HIS SER ALA SEQRES 19 A 240 ILE LYS LEU GLU LEU ARG SEQRES 1 B 240 MET THR GLY SER ASN SER HIS ILE THR ILE LEU THR LEU SEQRES 2 B 240 ASN ILE ASN GLY LEU ASN SER ALA ILE LYS ARG HIS ARG SEQRES 3 B 240 LEU ALA SER TRP ILE LYS SER GLN ASP PRO SER VAL CYS SEQRES 4 B 240 CYS ILE GLN GLU THR HIS LEU THR CYS ARG ASP THR HIS SEQRES 5 B 240 ARG LEU LYS ILE LYS GLY TRP ARG LYS ILE TYR GLN ALA SEQRES 6 B 240 ASN GLY LYS GLN LYS LYS ALA GLY VAL ALA ILE LEU VAL SEQRES 7 B 240 SER ASP LYS THR ASP PHE LYS PRO THR LYS ILE LYS ARG SEQRES 8 B 240 ASP LYS GLU GLY HIS TYR ILE MET VAL LYS GLY SER ILE SEQRES 9 B 240 GLN GLN GLU GLU LEU THR ILE LEU ASN ILE TYR ALA PRO SEQRES 10 B 240 ASN THR GLY ALA PRO ARG PHE ILE LYS GLN VAL LEU SER SEQRES 11 B 240 ASP LEU GLN ARG ASP LEU ASP SER HIS THR LEU ILE MET SEQRES 12 B 240 GLY ASP PHE ASN THR PRO LEU SER THR LEU ASP ARG SER SEQRES 13 B 240 THR ARG GLN LYS VAL ASN LYS ASP THR GLN GLU LEU ASN SEQRES 14 B 240 SER ALA LEU HIS GLN ALA ASP LEU ILE ASP ILE TYR ARG SEQRES 15 B 240 THR LEU HIS PRO LYS SER THR GLU TYR THR TYR VAL ARG SEQRES 16 B 240 VAL ARG ASP GLY HIS VAL SER GLN SER LYS ILE ASP HIS SEQRES 17 B 240 ILE VAL GLY SER LYS ALA LEU LEU SER LYS CYS LYS ARG SEQRES 18 B 240 THR GLU ILE ILE THR ASN TYR LEU SER ASP HIS SER ALA SEQRES 19 B 240 ILE LYS LEU GLU LEU ARG HET SO4 A1241 5 HET SO4 A1242 5 HET SO4 A1243 5 HET SO4 A1244 5 HET SO4 B1240 5 HET SO4 B1241 5 HETNAM SO4 SULFATE ION FORMUL 3 SO4 6(O4 S 2-) FORMUL 4 HOH *155(H2 O) HELIX 1 1 SER A 20 ASP A 35 1 16 HELIX 2 2 ARG A 49 LEU A 54 5 6 HELIX 3 3 GLY A 120 LEU A 132 1 13 HELIX 4 4 GLN A 133 LEU A 136 5 4 HELIX 5 5 SER A 151 ARG A 155 5 5 HELIX 6 6 ASN A 162 ALA A 175 1 14 HELIX 7 7 ILE A 180 HIS A 185 1 6 HELIX 8 8 ALA A 214 SER A 217 5 4 HELIX 9 9 SER B 20 ASP B 35 1 16 HELIX 10 10 ARG B 49 LEU B 54 5 6 HELIX 11 11 GLY B 120 LEU B 132 1 13 HELIX 12 12 GLN B 133 LEU B 136 5 4 HELIX 13 13 SER B 151 ARG B 155 5 5 HELIX 14 14 ASN B 162 ALA B 175 1 14 HELIX 15 15 ILE B 180 HIS B 185 1 6 HELIX 16 16 ALA B 214 CYS B 219 5 6 SHEET 1 AA 6 LYS A 61 ALA A 65 0 SHEET 2 AA 6 VAL A 74 VAL A 78 -1 O VAL A 74 N ALA A 65 SHEET 3 AA 6 VAL A 38 GLN A 42 -1 O CYS A 39 N LEU A 77 SHEET 4 AA 6 ILE A 8 ASN A 14 1 O THR A 9 N VAL A 38 SHEET 5 AA 6 ALA A 234 LEU A 239 -1 O ILE A 235 N THR A 12 SHEET 6 AA 6 CYS A 219 ILE A 225 -1 N LYS A 220 O GLU A 238 SHEET 1 AB 6 PHE A 84 ARG A 91 0 SHEET 2 AB 6 TYR A 97 ILE A 104 -1 O MET A 99 N LYS A 90 SHEET 3 AB 6 GLU A 107 TYR A 115 -1 O GLU A 107 N ILE A 104 SHEET 4 AB 6 THR A 140 ASP A 145 1 O LEU A 141 N LEU A 112 SHEET 5 AB 6 ASP A 207 SER A 212 -1 O HIS A 208 N GLY A 144 SHEET 6 AB 6 LEU A 177 ASP A 179 -1 O ILE A 178 N GLY A 211 SHEET 1 AC 2 TYR A 193 ARG A 197 0 SHEET 2 AC 2 HIS A 200 SER A 204 -1 O HIS A 200 N ARG A 197 SHEET 1 BA 6 LYS B 61 ALA B 65 0 SHEET 2 BA 6 VAL B 74 VAL B 78 -1 O VAL B 74 N ALA B 65 SHEET 3 BA 6 VAL B 38 GLN B 42 -1 O CYS B 39 N LEU B 77 SHEET 4 BA 6 ILE B 8 ASN B 14 1 O LEU B 11 N CYS B 40 SHEET 5 BA 6 ALA B 234 LEU B 239 -1 O ILE B 235 N THR B 12 SHEET 6 BA 6 THR B 222 ILE B 225 -1 O GLU B 223 N LYS B 236 SHEET 1 BB 6 PHE B 84 ARG B 91 0 SHEET 2 BB 6 TYR B 97 ILE B 104 -1 O MET B 99 N LYS B 90 SHEET 3 BB 6 GLU B 107 TYR B 115 -1 O GLU B 107 N ILE B 104 SHEET 4 BB 6 THR B 140 ASP B 145 1 O LEU B 141 N LEU B 112 SHEET 5 BB 6 ASP B 207 SER B 212 -1 O HIS B 208 N GLY B 144 SHEET 6 BB 6 LEU B 177 ASP B 179 -1 O ILE B 178 N GLY B 211 SHEET 1 BC 2 TYR B 193 ARG B 197 0 SHEET 2 BC 2 HIS B 200 SER B 204 -1 O HIS B 200 N ARG B 197 SITE 1 AC1 5 ASN A 16 GLY A 17 LEU A 18 ASN A 19 SITE 2 AC1 5 HIS A 45 SITE 1 AC2 5 HIS A 45 LYS A 71 ALA A 72 TYR A 115 SITE 2 AC2 5 HOH A2023 SITE 1 AC3 7 GLU A 43 TYR A 115 ASN A 118 ASP A 145 SITE 2 AC3 7 TYR A 193 HIS A 232 HOH A2078 SITE 1 AC4 4 PRO A 149 ARG A 155 HOH A2045 HOH A2079 SITE 1 AC5 4 HIS B 45 LYS B 71 ALA B 72 TYR B 115 SITE 1 AC6 5 GLY B 17 LEU B 18 ASN B 19 HIS B 45 SITE 2 AC6 5 HOH B2076 CRYST1 54.726 70.142 130.221 90.00 90.00 90.00 P 21 21 21 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 0.018273 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014257 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007679 0.00000