HEADER TRANSFERASE, LYASE/DNA 14-NOV-13 4NLK TITLE STRUCTURE OF HUMAN DNA POLYMERASE BETA COMPLEXED WITH 8BRG IN THE TITLE 2 TEMPLATE BASE-PAIRED WITH INCOMING NON-HYDROLYZABLE CTP COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*CP*CP*GP*AP*CP*(BGM)P*TP*CP*GP*CP*AP*TP*CP*AP*GP*C)- COMPND 3 3'; COMPND 4 CHAIN: T; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: TEMPLATE; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: 5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*A)-3'; COMPND 9 CHAIN: P; COMPND 10 ENGINEERED: YES; COMPND 11 OTHER_DETAILS: UP PRIMER; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: 5'-D(P*GP*TP*CP*GP*G)-3'; COMPND 14 CHAIN: D; COMPND 15 ENGINEERED: YES; COMPND 16 OTHER_DETAILS: DOWN PRIMER; COMPND 17 MOL_ID: 4; COMPND 18 MOLECULE: DNA POLYMERASE BETA; COMPND 19 CHAIN: A; COMPND 20 EC: 2.7.7.7, 4.2.99.-; COMPND 21 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES; SOURCE 5 MOL_ID: 3; SOURCE 6 SYNTHETIC: YES; SOURCE 7 MOL_ID: 4; SOURCE 8 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 9 ORGANISM_COMMON: HUMAN; SOURCE 10 ORGANISM_TAXID: 9606; SOURCE 11 GENE: POLB; SOURCE 12 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 13 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS DNA BINDING, HELIX-TURN-HELIX MOTIF, POLYMERASE FOLD, NUCLEOTIDYL KEYWDS 2 TRANSFERASE, NUCLEUS, TRANSFERASE, LYASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.-C.KOAG,K.MIN,A.F.MONZINGO,S.LEE REVDAT 4 28-FEB-24 4NLK 1 REMARK LINK REVDAT 3 19-MAR-14 4NLK 1 JRNL REVDAT 2 12-FEB-14 4NLK 1 JRNL REVDAT 1 22-JAN-14 4NLK 0 JRNL AUTH M.C.KOAG,K.MIN,S.LEE JRNL TITL STRUCTURAL BASIS FOR PROMUTAGENICITY OF 8-HALOGENATED JRNL TITL 2 GUANINE. JRNL REF J.BIOL.CHEM. V. 289 6289 2014 JRNL REFN ISSN 0021-9258 JRNL PMID 24425881 JRNL DOI 10.1074/JBC.M113.537803 REMARK 2 REMARK 2 RESOLUTION. 2.49 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0117 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) : 2.49 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 53.01 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.9 REMARK 3 NUMBER OF REFLECTIONS : 14227 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) : 0.197 REMARK 3 R VALUE (WORKING SET) : 0.194 REMARK 3 FREE R VALUE : 0.270 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 715 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) : 2.49 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.56 REMARK 3 REFLECTION IN BIN (WORKING SET) : 743 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 74.20 REMARK 3 BIN R VALUE (WORKING SET) : 0.3070 REMARK 3 BIN FREE R VALUE SET COUNT : 48 REMARK 3 BIN FREE R VALUE : 0.3170 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2608 REMARK 3 NUCLEIC ACID ATOMS : 633 REMARK 3 HETEROGEN ATOMS : 32 REMARK 3 SOLVENT ATOMS : 66 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.54000 REMARK 3 B22 (A**2) : -0.29000 REMARK 3 B33 (A**2) : -0.61000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 1.03000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 2.304 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.345 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.242 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 11.054 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.938 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.864 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3394 ; 0.011 ; 0.018 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4707 ; 1.659 ; 1.854 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 325 ; 6.055 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 125 ;38.606 ;24.240 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 506 ;17.438 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 18 ;20.224 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 488 ; 0.099 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2325 ; 0.007 ; 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN USED IF PRESENT IN REMARK 3 THE INPUT REMARK 4 REMARK 4 4NLK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-NOV-13. REMARK 100 THE DEPOSITION ID IS D_1000083355. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-JUL-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 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) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14564 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.494 REMARK 200 RESOLUTION RANGE LOW (A) : 53.010 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.49 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL 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 (%): 46.05 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.28 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 14-23% PEG3400, 350 MM SODIUM ACETATE, REMARK 280 50 MM IMIDAZOLE, PH 7.5, VAPOR DIFFUSION, SITTING DROP REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 39.85300 REMARK 290 SMTRY3 2 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5710 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19880 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -71.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: T, P, D, 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 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 PRO A 7 REMARK 465 GLN A 8 REMARK 465 GLU A 9 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 248 CG CD CE NZ REMARK 470 VAL A 303 CG1 CG2 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 N LYS A 244 OE2 GLU A 247 1.48 REMARK 500 CA LYS A 244 OE2 GLU A 247 1.81 REMARK 500 CB LYS A 244 OE2 GLU A 247 1.90 REMARK 500 CB ASP A 160 O HOH A 518 1.91 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 DG D 1 P DG D 1 OP3 -0.124 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 DC T 10 C3' - O3' - P ANGL. DEV. = 11.1 DEGREES REMARK 500 DT T 12 C3' - O3' - P ANGL. DEV. = 9.5 DEGREES REMARK 500 DG P 4 C3' - O3' - P ANGL. DEV. = 11.5 DEGREES REMARK 500 DC P 8 C3' - O3' - P ANGL. DEV. = 8.4 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 PRO A 50 37.29 -89.05 REMARK 500 CYS A 178 -147.18 -116.34 REMARK 500 ASP A 246 -11.35 79.30 REMARK 500 ASN A 294 -166.58 -118.79 REMARK 500 PRO A 310 123.63 -37.48 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 NA A 403 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG P 9 OP1 REMARK 620 2 DG P 9 OP2 52.6 REMARK 620 3 THR A 101 O 171.1 136.2 REMARK 620 4 VAL A 103 O 91.2 139.4 80.8 REMARK 620 5 ILE A 106 O 94.6 88.0 87.3 76.0 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 402 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DA P 10 O3' REMARK 620 2 ASP A 190 OD2 152.0 REMARK 620 3 ASP A 192 OD1 81.3 96.9 REMARK 620 4 ASP A 256 OD2 66.3 85.8 81.6 REMARK 620 5 0KX A 405 O2A 108.2 99.7 88.4 169.1 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 404 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DC D 3 OP1 REMARK 620 2 LYS A 60 O 164.0 REMARK 620 3 LEU A 62 O 91.3 91.4 REMARK 620 4 VAL A 65 O 96.4 67.8 90.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 401 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 190 OD1 REMARK 620 2 ASP A 192 OD2 94.9 REMARK 620 3 0KX A 405 O2G 86.7 163.1 REMARK 620 4 0KX A 405 O2A 97.9 100.4 96.1 REMARK 620 5 0KX A 405 O1B 163.4 94.3 80.5 94.0 REMARK 620 6 HOH A 502 O 77.9 82.6 81.3 175.1 89.6 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 MG A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 0KX A 405 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1BPX RELATED DB: PDB REMARK 900 RELATED ID: 3ISB RELATED DB: PDB REMARK 900 RELATED ID: 4NLN RELATED DB: PDB REMARK 900 RELATED ID: 4NLZ RELATED DB: PDB REMARK 900 RELATED ID: 4NM1 RELATED DB: PDB REMARK 900 RELATED ID: 4NM2 RELATED DB: PDB DBREF 4NLK A 7 335 UNP P06746 DPOLB_HUMAN 7 335 DBREF 4NLK T 1 16 PDB 4NLK 4NLK 1 16 DBREF 4NLK P 1 10 PDB 4NLK 4NLK 1 10 DBREF 4NLK D 1 5 PDB 4NLK 4NLK 1 5 SEQRES 1 T 16 DC DC DG DA DC BGM DT DC DG DC DA DT DC SEQRES 2 T 16 DA DG DC SEQRES 1 P 10 DG DC DT DG DA DT DG DC DG DA SEQRES 1 D 5 DG DT DC DG DG SEQRES 1 A 329 PRO GLN GLU THR LEU ASN GLY GLY ILE THR ASP MET LEU SEQRES 2 A 329 THR GLU LEU ALA ASN PHE GLU LYS ASN VAL SER GLN ALA SEQRES 3 A 329 ILE HIS LYS TYR ASN ALA TYR ARG LYS ALA ALA SER VAL SEQRES 4 A 329 ILE ALA LYS TYR PRO HIS LYS ILE LYS SER GLY ALA GLU SEQRES 5 A 329 ALA LYS LYS LEU PRO GLY VAL GLY THR LYS ILE ALA GLU SEQRES 6 A 329 LYS ILE ASP GLU PHE LEU ALA THR GLY LYS LEU ARG LYS SEQRES 7 A 329 LEU GLU LYS ILE ARG GLN ASP ASP THR SER SER SER ILE SEQRES 8 A 329 ASN PHE LEU THR ARG VAL SER GLY ILE GLY PRO SER ALA SEQRES 9 A 329 ALA ARG LYS PHE VAL ASP GLU GLY ILE LYS THR LEU GLU SEQRES 10 A 329 ASP LEU ARG LYS ASN GLU ASP LYS LEU ASN HIS HIS GLN SEQRES 11 A 329 ARG ILE GLY LEU LYS TYR PHE GLY ASP PHE GLU LYS ARG SEQRES 12 A 329 ILE PRO ARG GLU GLU MET LEU GLN MET GLN ASP ILE VAL SEQRES 13 A 329 LEU ASN GLU VAL LYS LYS VAL ASP SER GLU TYR ILE ALA SEQRES 14 A 329 THR VAL CYS GLY SER PHE ARG ARG GLY ALA GLU SER SER SEQRES 15 A 329 GLY ASP MET ASP VAL LEU LEU THR HIS PRO SER PHE THR SEQRES 16 A 329 SER GLU SER THR LYS GLN PRO LYS LEU LEU HIS GLN VAL SEQRES 17 A 329 VAL GLU GLN LEU GLN LYS VAL HIS PHE ILE THR ASP THR SEQRES 18 A 329 LEU SER LYS GLY GLU THR LYS PHE MET GLY VAL CYS GLN SEQRES 19 A 329 LEU PRO SER LYS ASN ASP GLU LYS GLU TYR PRO HIS ARG SEQRES 20 A 329 ARG ILE ASP ILE ARG LEU ILE PRO LYS ASP GLN TYR TYR SEQRES 21 A 329 CYS GLY VAL LEU TYR PHE THR GLY SER ASP ILE PHE ASN SEQRES 22 A 329 LYS ASN MET ARG ALA HIS ALA LEU GLU LYS GLY PHE THR SEQRES 23 A 329 ILE ASN GLU TYR THR ILE ARG PRO LEU GLY VAL THR GLY SEQRES 24 A 329 VAL ALA GLY GLU PRO LEU PRO VAL ASP SER GLU LYS ASP SEQRES 25 A 329 ILE PHE ASP TYR ILE GLN TRP LYS TYR ARG GLU PRO LYS SEQRES 26 A 329 ASP ARG SER GLU MODRES 4NLK BGM T 6 DG HET BGM T 6 23 HET MG A 401 1 HET MG A 402 1 HET NA A 403 1 HET NA A 404 1 HET 0KX A 405 28 HETNAM BGM 8-BROMO-2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM NA SODIUM ION HETNAM 0KX 2'-DEOXY-5'-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY) HETNAM 2 0KX PHOSPHORYL]AMINO}PHOSPHORYL]CYTIDINE FORMUL 1 BGM C10 H13 BR N5 O7 P FORMUL 5 MG 2(MG 2+) FORMUL 7 NA 2(NA 1+) FORMUL 9 0KX C9 H17 N4 O12 P3 FORMUL 10 HOH *66(H2 O) HELIX 1 1 ASN A 12 VAL A 29 1 18 HELIX 2 2 ALA A 32 LYS A 48 1 17 HELIX 3 3 SER A 55 LYS A 61 1 7 HELIX 4 4 GLY A 66 GLY A 80 1 15 HELIX 5 5 LEU A 82 ASP A 91 1 10 HELIX 6 6 ASP A 91 ARG A 102 1 12 HELIX 7 7 GLY A 107 GLU A 117 1 11 HELIX 8 8 THR A 121 LYS A 127 1 7 HELIX 9 9 ASN A 128 LEU A 132 5 5 HELIX 10 10 ASN A 133 TYR A 142 1 10 HELIX 11 11 TYR A 142 GLU A 147 1 6 HELIX 12 12 ARG A 152 ASP A 170 1 19 HELIX 13 13 CYS A 178 ARG A 183 1 6 HELIX 14 14 LEU A 211 VAL A 221 1 11 HELIX 15 15 PRO A 261 ASP A 263 5 3 HELIX 16 16 GLN A 264 GLY A 274 1 11 HELIX 17 17 SER A 275 LYS A 289 1 15 HELIX 18 18 SER A 315 ILE A 323 1 9 HELIX 19 19 GLU A 329 ARG A 333 5 5 SHEET 1 A 2 ILE A 150 PRO A 151 0 SHEET 2 A 2 SER A 187 SER A 188 -1 O SER A 188 N ILE A 150 SHEET 1 B 5 ILE A 174 VAL A 177 0 SHEET 2 B 5 MET A 191 THR A 196 -1 O LEU A 194 N THR A 176 SHEET 3 B 5 ARG A 253 LEU A 259 1 O ARG A 258 N LEU A 195 SHEET 4 B 5 LYS A 234 CYS A 239 -1 N PHE A 235 O ILE A 257 SHEET 5 B 5 ILE A 224 LYS A 230 -1 N LEU A 228 O MET A 236 SHEET 1 C 2 PHE A 291 ILE A 293 0 SHEET 2 C 2 ILE A 298 PRO A 300 -1 O ARG A 299 N THR A 292 LINK O3' DC T 5 P BGM T 6 1555 1555 1.63 LINK O3' BGM T 6 P DT T 7 1555 1555 1.60 LINK OP1 DG P 9 NA NA A 403 1555 1555 2.42 LINK OP2 DG P 9 NA NA A 403 1555 1555 3.17 LINK O3' DA P 10 MG MG A 402 1555 1555 2.61 LINK OP1 DC D 3 NA NA A 404 1555 1555 2.32 LINK O LYS A 60 NA NA A 404 1555 1555 2.39 LINK O LEU A 62 NA NA A 404 1555 1555 2.77 LINK O VAL A 65 NA NA A 404 1555 1555 2.64 LINK O THR A 101 NA NA A 403 1555 1555 2.16 LINK O VAL A 103 NA NA A 403 1555 1555 2.94 LINK O ILE A 106 NA NA A 403 1555 1555 2.45 LINK OD1 ASP A 190 MG MG A 401 1555 1555 1.95 LINK OD2 ASP A 190 MG MG A 402 1555 1555 1.97 LINK OD2 ASP A 192 MG MG A 401 1555 1555 2.03 LINK OD1 ASP A 192 MG MG A 402 1555 1555 2.37 LINK OD2 ASP A 256 MG MG A 402 1555 1555 2.30 LINK MG MG A 401 O2G 0KX A 405 1555 1555 1.93 LINK MG MG A 401 O2A 0KX A 405 1555 1555 1.95 LINK MG MG A 401 O1B 0KX A 405 1555 1555 1.96 LINK MG MG A 401 O HOH A 502 1555 1555 2.40 LINK MG MG A 402 O2A 0KX A 405 1555 1555 2.16 CISPEP 1 GLY A 274 SER A 275 0 14.62 SITE 1 AC1 5 ASP A 190 ASP A 192 MG A 402 0KX A 405 SITE 2 AC1 5 HOH A 502 SITE 1 AC2 6 ASP A 190 ASP A 192 ASP A 256 MG A 401 SITE 2 AC2 6 0KX A 405 DA P 10 SITE 1 AC3 4 THR A 101 VAL A 103 ILE A 106 DG P 9 SITE 1 AC4 4 LYS A 60 LEU A 62 VAL A 65 DC D 3 SITE 1 AC5 21 GLY A 179 SER A 180 ARG A 183 SER A 188 SITE 2 AC5 21 GLY A 189 ASP A 190 ASP A 192 TYR A 271 SITE 3 AC5 21 PHE A 272 THR A 273 GLY A 274 ASP A 276 SITE 4 AC5 21 ASN A 279 MG A 401 MG A 402 HOH A 502 SITE 5 AC5 21 HOH A 506 HOH A 522 HOH A 552 DA P 10 SITE 6 AC5 21 BGM T 6 CRYST1 50.807 79.706 55.683 90.00 107.83 90.00 P 1 21 1 2 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 0.019682 0.000000 0.006329 0.00000 SCALE2 0.000000 0.012546 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018864 0.00000