PDB Short entry for 4RQ5 HEADER TRANSFERASE/DNA 31-OCT-14 4RQ5 TITLE HUMAN DNA POLYMERASE BETA WITH GAPPED DNA CONTAINING AN 8-OXO-7,8- TITLE 2 DIHYDRO-GUANINE (8-OXOG)AND DATP SOAKED WITH MGCL2 FOR 60 S COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE BETA; COMPND 3 CHAIN: A; COMPND 4 EC: 2.7.7.7, 4.2.99.-; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DNA (5'-D(P*GP*TP*CP*GP*G)-3'); COMPND 8 CHAIN: D; COMPND 9 SYNONYM: 5-MER PHOSPHORYLATED DOWNSTREAM PRIMER; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*CP*A)-3'); COMPND 13 CHAIN: P; COMPND 14 SYNONYM: 10-MER PRIMER; COMPND 15 ENGINEERED: YES; COMPND 16 MOL_ID: 4; COMPND 17 MOLECULE: DNA (5'-D(*CP*CP*GP*AP*CP*(8OG) COMPND 18 P*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'); COMPND 19 CHAIN: T; COMPND 20 SYNONYM: 16-MER TEMPLATE; COMPND 21 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: POL B, POLB; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28B; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 14 ORGANISM_TAXID: 32630; SOURCE 15 MOL_ID: 3; SOURCE 16 SYNTHETIC: YES; SOURCE 17 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 18 ORGANISM_TAXID: 32630; SOURCE 19 MOL_ID: 4; SOURCE 20 SYNTHETIC: YES; SOURCE 21 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 22 ORGANISM_TAXID: 32630 KEYWDS X-FAMILY, POL BETA, TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR R.VYAS,Z.SUO REVDAT 3 28-FEB-24 4RQ5 1 REMARK SEQADV LINK REVDAT 2 06-MAY-15 4RQ5 1 JRNL REVDAT 1 15-APR-15 4RQ5 0 JRNL AUTH R.VYAS,A.J.REED,E.J.TOKARSKY,Z.SUO JRNL TITL VIEWING HUMAN DNA POLYMERASE BETA FAITHFULLY AND JRNL TITL 2 UNFAITHFULLY BYPASS AN OXIDATIVE LESION BY TIME-DEPENDENT JRNL TITL 3 CRYSTALLOGRAPHY. JRNL REF J.AM.CHEM.SOC. V. 137 5225 2015 JRNL REFN ISSN 0002-7863 JRNL PMID 25825995 JRNL DOI 10.1021/JACS.5B02109 REMARK 2 REMARK 2 RESOLUTION. 2.32 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0073 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) : 2.32 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 94.7 REMARK 3 NUMBER OF REFLECTIONS : 16065 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) : 0.200 REMARK 3 R VALUE (WORKING SET) : 0.196 REMARK 3 FREE R VALUE : 0.266 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 822 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) : 2.32 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.38 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1050 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 86.06 REMARK 3 BIN R VALUE (WORKING SET) : 0.3040 REMARK 3 BIN FREE R VALUE SET COUNT : 61 REMARK 3 BIN FREE R VALUE : 0.3730 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2613 REMARK 3 NUCLEIC ACID ATOMS : 654 REMARK 3 HETEROGEN ATOMS : 54 REMARK 3 SOLVENT ATOMS : 76 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 39.17 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.30000 REMARK 3 B22 (A**2) : 0.49000 REMARK 3 B33 (A**2) : -1.94000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.83000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.564 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.295 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.257 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 11.742 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.948 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.907 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3483 ; 0.009 ; 0.018 REMARK 3 BOND LENGTHS OTHERS (A): 2981 ; 0.004 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4807 ; 1.413 ; 1.807 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6908 ; 0.890 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 325 ; 6.099 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 125 ;38.185 ;24.240 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 511 ;15.680 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 18 ;15.330 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 492 ; 0.067 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3395 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 776 ; 0.001 ; 0.020 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): 1305 ; 2.204 ; 3.693 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1302 ; 2.198 ; 3.686 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1627 ; 3.632 ; 5.529 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1628 ; 3.631 ; 5.531 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2178 ; 2.503 ; 4.097 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2179 ; 2.503 ; 4.097 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3181 ; 4.092 ; 6.089 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 4252 ; 6.103 ;32.085 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 4253 ; 6.102 ;32.084 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 ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 4RQ5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-NOV-14. REMARK 100 THE DEPOSITION ID IS D_1000087658. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-JUL-14 REMARK 200 TEMPERATURE (KELVIN) : 193 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 31-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97931 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX225HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16913 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.320 REMARK 200 RESOLUTION RANGE LOW (A) : 79.700 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.3 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : 0.08100 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.32 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.45 REMARK 200 COMPLETENESS FOR SHELL (%) : 88.2 REMARK 200 DATA REDUNDANCY IN SHELL : 2.70 REMARK 200 R MERGE FOR SHELL (I) : 0.77600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.02 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.12 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50 MM IMIDAZOLE, 350 MM SODIUM REMARK 280 ACETATE, 17% PEG3350, PH 8.0, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 295K 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 39.85100 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: 7680 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20010 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -108.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, D, P, T 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 GLY A 0 REMARK 465 MET A 1 REMARK 465 SER A 2 REMARK 465 LYS A 3 REMARK 465 ARG A 4 REMARK 465 LYS A 5 REMARK 465 ALA A 6 REMARK 465 PRO A 7 REMARK 465 GLN A 8 REMARK 465 GLU A 9 REMARK 465 HIS A 336 REMARK 465 HIS A 337 REMARK 465 HIS A 338 REMARK 465 HIS A 339 REMARK 465 HIS A 340 REMARK 465 HIS A 341 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 N7 DA P 5 O HOH P 201 2.19 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 -0.125 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 DG P 7 C1' - O4' - C4' ANGL. DEV. = -6.0 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 ASN A 133 -178.05 -66.00 REMARK 500 ASP A 170 121.37 179.77 REMARK 500 CYS A 178 -139.75 -104.21 REMARK 500 SER A 199 3.02 -61.79 REMARK 500 SER A 204 167.33 162.92 REMARK 500 ASP A 246 -9.56 75.17 REMARK 500 THR A 304 5.44 -59.65 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 404 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS A 60 O REMARK 620 2 LEU A 62 O 85.2 REMARK 620 3 VAL A 65 O 99.4 97.6 REMARK 620 4 DC D 3 OP1 175.4 90.2 81.4 REMARK 620 N 1 2 3 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 THR A 101 O REMARK 620 2 VAL A 103 O 81.7 REMARK 620 3 ILE A 106 O 81.7 75.9 REMARK 620 4 HOH A 503 O 83.5 72.3 146.5 REMARK 620 5 DG P 9 OP1 157.7 80.2 81.4 102.9 REMARK 620 N 1 2 3 4 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 OD2 REMARK 620 2 ASP A 192 OD1 102.1 REMARK 620 3 ASP A 256 OD2 83.3 95.3 REMARK 620 4 DTP A 410 O2A 99.3 85.7 176.9 REMARK 620 5 HOH A 546 O 70.3 170.5 89.6 89.8 REMARK 620 6 DC P 10 O3' 143.2 112.9 103.7 73.3 73.6 REMARK 620 7 DC P 10 O3' 160.5 91.1 81.3 95.8 97.7 33.3 REMARK 620 8 DA P 11 OP1 105.9 90.4 168.0 9.0 86.4 64.3 88.1 REMARK 620 N 1 2 3 4 5 6 7 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 ASP A 190 OD1 REMARK 620 2 ASP A 192 OD2 106.5 REMARK 620 3 PPV A 409 O12 82.0 166.1 REMARK 620 4 PPV A 409 O21 155.4 98.0 73.6 REMARK 620 5 DTP A 410 O2A 80.6 85.2 107.5 103.9 REMARK 620 6 DTP A 410 O2G 79.6 169.2 20.4 76.6 87.1 REMARK 620 7 DTP A 410 O2B 165.7 87.7 84.5 11.0 99.4 86.2 REMARK 620 8 DTP A 410 O3A 111.0 121.5 63.2 55.1 59.5 47.8 58.2 REMARK 620 9 HOH A 547 O 102.0 85.7 81.6 77.5 170.9 101.9 80.3 126.2 REMARK 620 N 1 2 3 4 5 6 7 8 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG P 101 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PPV A 409 O11 REMARK 620 2 DTP A 410 O1A 76.2 REMARK 620 3 DTP A 410 O3A 13.3 70.1 REMARK 620 4 HOH A 559 O 80.6 154.8 89.0 REMARK 620 5 DA P 11 OP2 75.9 13.3 72.8 146.9 REMARK 620 6 HOH P 202 O 83.7 83.8 94.7 84.1 70.6 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 ACT A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 407 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 408 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PPV A 409 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DTP A 410 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG P 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4RPX RELATED DB: PDB REMARK 900 RELATED ID: 4RPY RELATED DB: PDB REMARK 900 RELATED ID: 4RPZ RELATED DB: PDB REMARK 900 RELATED ID: 4RQ0 RELATED DB: PDB REMARK 900 RELATED ID: 4RQ1 RELATED DB: PDB REMARK 900 RELATED ID: 4RQ2 RELATED DB: PDB REMARK 900 RELATED ID: 4RQ3 RELATED DB: PDB REMARK 900 RELATED ID: 4RQ4 RELATED DB: PDB REMARK 900 RELATED ID: 4RQ6 RELATED DB: PDB REMARK 900 RELATED ID: 4RQ7 RELATED DB: PDB REMARK 900 RELATED ID: 4RQ8 RELATED DB: PDB DBREF 4RQ5 A 1 335 UNP P06746 DPOLB_HUMAN 1 335 DBREF 4RQ5 D 1 5 PDB 4RQ5 4RQ5 1 5 DBREF 4RQ5 P 1 11 PDB 4RQ5 4RQ5 1 11 DBREF 4RQ5 T 1 16 PDB 4RQ5 4RQ5 1 16 SEQADV 4RQ5 MET A -1 UNP P06746 EXPRESSION TAG SEQADV 4RQ5 GLY A 0 UNP P06746 EXPRESSION TAG SEQADV 4RQ5 HIS A 336 UNP P06746 EXPRESSION TAG SEQADV 4RQ5 HIS A 337 UNP P06746 EXPRESSION TAG SEQADV 4RQ5 HIS A 338 UNP P06746 EXPRESSION TAG SEQADV 4RQ5 HIS A 339 UNP P06746 EXPRESSION TAG SEQADV 4RQ5 HIS A 340 UNP P06746 EXPRESSION TAG SEQADV 4RQ5 HIS A 341 UNP P06746 EXPRESSION TAG SEQRES 1 A 343 MET GLY MET SER LYS ARG LYS ALA PRO GLN GLU THR LEU SEQRES 2 A 343 ASN GLY GLY ILE THR ASP MET LEU THR GLU LEU ALA ASN SEQRES 3 A 343 PHE GLU LYS ASN VAL SER GLN ALA ILE HIS LYS TYR ASN SEQRES 4 A 343 ALA TYR ARG LYS ALA ALA SER VAL ILE ALA LYS TYR PRO SEQRES 5 A 343 HIS LYS ILE LYS SER GLY ALA GLU ALA LYS LYS LEU PRO SEQRES 6 A 343 GLY VAL GLY THR LYS ILE ALA GLU LYS ILE ASP GLU PHE SEQRES 7 A 343 LEU ALA THR GLY LYS LEU ARG LYS LEU GLU LYS ILE ARG SEQRES 8 A 343 GLN ASP ASP THR SER SER SER ILE ASN PHE LEU THR ARG SEQRES 9 A 343 VAL SER GLY ILE GLY PRO SER ALA ALA ARG LYS PHE VAL SEQRES 10 A 343 ASP GLU GLY ILE LYS THR LEU GLU ASP LEU ARG LYS ASN SEQRES 11 A 343 GLU ASP LYS LEU ASN HIS HIS GLN ARG ILE GLY LEU LYS SEQRES 12 A 343 TYR PHE GLY ASP PHE GLU LYS ARG ILE PRO ARG GLU GLU SEQRES 13 A 343 MET LEU GLN MET GLN ASP ILE VAL LEU ASN GLU VAL LYS SEQRES 14 A 343 LYS VAL ASP SER GLU TYR ILE ALA THR VAL CYS GLY SER SEQRES 15 A 343 PHE ARG ARG GLY ALA GLU SER SER GLY ASP MET ASP VAL SEQRES 16 A 343 LEU LEU THR HIS PRO SER PHE THR SER GLU SER THR LYS SEQRES 17 A 343 GLN PRO LYS LEU LEU HIS GLN VAL VAL GLU GLN LEU GLN SEQRES 18 A 343 LYS VAL HIS PHE ILE THR ASP THR LEU SER LYS GLY GLU SEQRES 19 A 343 THR LYS PHE MET GLY VAL CYS GLN LEU PRO SER LYS ASN SEQRES 20 A 343 ASP GLU LYS GLU TYR PRO HIS ARG ARG ILE ASP ILE ARG SEQRES 21 A 343 LEU ILE PRO LYS ASP GLN TYR TYR CYS GLY VAL LEU TYR SEQRES 22 A 343 PHE THR GLY SER ASP ILE PHE ASN LYS ASN MET ARG ALA SEQRES 23 A 343 HIS ALA LEU GLU LYS GLY PHE THR ILE ASN GLU TYR THR SEQRES 24 A 343 ILE ARG PRO LEU GLY VAL THR GLY VAL ALA GLY GLU PRO SEQRES 25 A 343 LEU PRO VAL ASP SER GLU LYS ASP ILE PHE ASP TYR ILE SEQRES 26 A 343 GLN TRP LYS TYR ARG GLU PRO LYS ASP ARG SER GLU HIS SEQRES 27 A 343 HIS HIS HIS HIS HIS SEQRES 1 D 5 DG DT DC DG DG SEQRES 1 P 11 DG DC DT DG DA DT DG DC DG DC DA SEQRES 1 T 16 DC DC DG DA DC 8OG DG DC DG DC DA DT DC SEQRES 2 T 16 DA DG DC MODRES 4RQ5 8OG T 6 DG HET 8OG T 6 23 HET MG A 401 1 HET MG A 402 1 HET NA A 403 1 HET NA A 404 1 HET ACT A 405 4 HET ACT A 406 4 HET CL A 407 1 HET CL A 408 1 HET PPV A 409 9 HET DTP A 410 30 HET MG P 101 1 HETNAM 8OG 8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM NA SODIUM ION HETNAM ACT ACETATE ION HETNAM CL CHLORIDE ION HETNAM PPV PYROPHOSPHATE HETNAM DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE HETSYN 8OG 8-OXO-7,8-DIHYDRO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE FORMUL 4 8OG C10 H14 N5 O8 P FORMUL 5 MG 3(MG 2+) FORMUL 7 NA 2(NA 1+) FORMUL 9 ACT 2(C2 H3 O2 1-) FORMUL 11 CL 2(CL 1-) FORMUL 13 PPV H4 O7 P2 FORMUL 14 DTP C10 H16 N5 O12 P3 FORMUL 16 HOH *76(H2 O) HELIX 1 1 ASN A 12 VAL A 29 1 18 HELIX 2 2 ALA A 32 TYR A 49 1 18 HELIX 3 3 SER A 55 LEU A 62 1 8 HELIX 4 4 GLY A 66 GLY A 80 1 15 HELIX 5 5 LEU A 82 GLN A 90 1 9 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 ASN A 128 1 8 HELIX 9 9 GLU A 129 LEU A 132 5 4 HELIX 10 10 ASN A 133 TYR A 142 1 10 HELIX 11 11 TYR A 142 LYS A 148 1 7 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 LYS A 209 VAL A 221 1 13 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 SER A 334 5 6 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 ASP A 226 O VAL A 238 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 8OG T 6 1555 1555 1.59 LINK O3' 8OG T 6 P DG T 7 1555 1555 1.58 LINK O LYS A 60 NA NA A 404 1555 1555 2.40 LINK O LEU A 62 NA NA A 404 1555 1555 2.57 LINK O VAL A 65 NA NA A 404 1555 1555 2.29 LINK O THR A 101 NA NA A 403 1555 1555 2.25 LINK O VAL A 103 NA NA A 403 1555 1555 2.69 LINK O ILE A 106 NA NA A 403 1555 1555 2.65 LINK OD2 ASP A 190 MG MG A 401 1555 1555 2.15 LINK OD1 ASP A 190 MG MG A 402 1555 1555 2.16 LINK OD1 ASP A 192 MG MG A 401 1555 1555 2.18 LINK OD2 ASP A 192 MG MG A 402 1555 1555 2.19 LINK OD2 ASP A 256 MG MG A 401 1555 1555 2.16 LINK MG MG A 401 O2ABDTP A 410 1555 1555 2.20 LINK MG MG A 401 O HOH A 546 1555 1555 2.18 LINK MG MG A 401 O3'A DC P 10 1555 1555 2.19 LINK MG MG A 401 O3'B DC P 10 1555 1555 2.19 LINK MG MG A 401 OP1A DA P 11 1555 1555 2.51 LINK MG MG A 402 O12APPV A 409 1555 1555 2.17 LINK MG MG A 402 O21APPV A 409 1555 1555 2.19 LINK MG MG A 402 O2ABDTP A 410 1555 1555 1.93 LINK MG MG A 402 O2GBDTP A 410 1555 1555 2.18 LINK MG MG A 402 O2BBDTP A 410 1555 1555 2.18 LINK MG MG A 402 O3ABDTP A 410 1555 1555 2.96 LINK MG MG A 402 O HOH A 547 1555 1555 2.18 LINK MG MG A 402 OP1A DA P 11 1555 1555 2.15 LINK NA NA A 403 O HOH A 503 1555 1555 2.42 LINK NA NA A 403 OP1 DG P 9 1555 1555 2.11 LINK NA NA A 404 OP1 DC D 3 1555 1555 2.67 LINK O11APPV A 409 MG MG P 101 1555 1555 2.21 LINK O1ABDTP A 410 MG MG P 101 1555 1555 2.17 LINK O3ABDTP A 410 MG MG P 101 1555 1555 2.19 LINK O HOH A 559 MG MG P 101 1555 1555 2.19 LINK OP2A DA P 11 MG MG P 101 1555 1555 2.18 LINK MG MG P 101 O HOH P 202 1555 1555 2.19 CISPEP 1 GLY A 274 SER A 275 0 -0.85 SITE 1 AC1 8 ASP A 190 ASP A 192 ASP A 256 MG A 402 SITE 2 AC1 8 DTP A 410 HOH A 546 DC P 10 DA P 11 SITE 1 AC2 7 ASP A 190 ASP A 192 MG A 401 PPV A 409 SITE 2 AC2 7 DTP A 410 HOH A 547 DA P 11 SITE 1 AC3 5 THR A 101 VAL A 103 ILE A 106 HOH A 503 SITE 2 AC3 5 DG P 9 SITE 1 AC4 4 LYS A 60 LEU A 62 VAL A 65 DC D 3 SITE 1 AC5 1 HOH A 514 SITE 1 AC6 3 PHE A 200 THR A 205 GLU A 232 SITE 1 AC7 3 ASN A 294 THR A 297 ARG A 299 SITE 1 AC8 3 GLN A 264 TYR A 266 CYS A 267 SITE 1 AC9 13 ARG A 149 GLY A 179 SER A 180 ARG A 183 SITE 2 AC9 13 GLY A 189 ASP A 190 ASP A 192 MG A 402 SITE 3 AC9 13 HOH A 547 HOH A 558 HOH A 559 MG P 101 SITE 4 AC9 13 HOH P 202 SITE 1 BC1 25 GLY A 179 SER A 180 ARG A 183 SER A 188 SITE 2 BC1 25 GLY A 189 ASP A 190 ASP A 192 TYR A 271 SITE 3 BC1 25 PHE A 272 THR A 273 GLY A 274 ASP A 276 SITE 4 BC1 25 ASN A 279 MG A 401 MG A 402 HOH A 546 SITE 5 BC1 25 HOH A 547 HOH A 558 HOH A 559 DC P 10 SITE 6 BC1 25 MG P 101 HOH P 202 HOH P 203 8OG T 6 SITE 7 BC1 25 DG T 7 SITE 1 BC2 5 PPV A 409 DTP A 410 HOH A 559 DA P 11 SITE 2 BC2 5 HOH P 202 CRYST1 49.212 79.702 55.384 90.00 106.66 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 0.020320 0.000000 0.006081 0.00000 SCALE2 0.000000 0.012547 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018847 0.00000