HEADER TRANSFERASE/DNA 09-OCT-18 6MQ8 TITLE BINARY STRUCTURE OF DNA POLYMERASE ETA IN COMPLEX WITH TEMPLATING TITLE 2 HYPOXANTHINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE ETA; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: RAD30 HOMOLOG A,XERODERMA PIGMENTOSUM VARIANT TYPE PROTEIN; COMPND 5 EC: 2.7.7.7; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA (5'-D(*CP*AP*TP*IP*AP*TP*GP*AP*CP*GP*CP*T)-3'); COMPND 9 CHAIN: T; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: DNA (5'-D(*AP*GP*CP*GP*TP*CP*AP*T)-3'); COMPND 13 CHAIN: P; COMPND 14 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: POLH, RAD30, RAD30A, XPV; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; 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 KEYWDS DNA POLYMERASE BETA, PROTEIN-DNA COMPLEX, HYPOXANTHINE, TRANSFERASE, KEYWDS 2 TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.A.HAWKINS,H.JUNG,S.LEE REVDAT 3 13-MAR-24 6MQ8 1 REMARK REVDAT 2 06-JAN-21 6MQ8 1 JRNL LINK REVDAT 1 23-OCT-19 6MQ8 0 JRNL AUTH H.JUNG,M.HAWKINS,S.LEE JRNL TITL STRUCTURAL INSIGHTS INTO THE BYPASS OF THE MAJOR DEAMINATED JRNL TITL 2 PURINES BY TRANSLESION SYNTHESIS DNA POLYMERASE. JRNL REF BIOCHEM.J. 2020 JRNL REFN ESSN 1470-8728 JRNL PMID 33258913 JRNL DOI 10.1042/BCJ20200800 REMARK 2 REMARK 2 RESOLUTION. 1.97 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.13_2998 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.97 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.27 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 31942 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.173 REMARK 3 R VALUE (WORKING SET) : 0.171 REMARK 3 FREE R VALUE : 0.208 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.270 REMARK 3 FREE R VALUE TEST SET COUNT : 2002 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 49.2849 - 4.7433 1.00 2183 146 0.1763 0.2089 REMARK 3 2 4.7433 - 3.7653 1.00 2163 144 0.1428 0.1722 REMARK 3 3 3.7653 - 3.2895 1.00 2138 144 0.1542 0.1907 REMARK 3 4 3.2895 - 2.9888 1.00 2147 144 0.1733 0.1851 REMARK 3 5 2.9888 - 2.7746 1.00 2141 145 0.1808 0.2313 REMARK 3 6 2.7746 - 2.6110 1.00 2136 143 0.1747 0.2181 REMARK 3 7 2.6110 - 2.4802 1.00 2145 142 0.1832 0.2220 REMARK 3 8 2.4802 - 2.3723 1.00 2132 144 0.1752 0.2037 REMARK 3 9 2.3723 - 2.2810 1.00 2135 144 0.1750 0.2107 REMARK 3 10 2.2810 - 2.2022 1.00 2128 145 0.1796 0.2285 REMARK 3 11 2.2022 - 2.1334 1.00 2111 134 0.1816 0.2326 REMARK 3 12 2.1334 - 2.0724 1.00 2146 146 0.1945 0.2306 REMARK 3 13 2.0724 - 2.0178 1.00 2141 139 0.2004 0.2629 REMARK 3 14 2.0178 - 1.9686 1.00 2094 142 0.2205 0.2836 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.490 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 25.57 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.48 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6MQ8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-OCT-18. REMARK 100 THE DEPOSITION ID IS D_1000237343. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-JUN-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 23-ID-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31977 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.970 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 5.100 REMARK 200 R MERGE (I) : 0.08300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.97 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.10 REMARK 200 R MERGE FOR SHELL (I) : 0.53400 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: PHASER 2.8.1 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.76 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM MES 5.5, 10% PEG 2K MME, 5MM REMARK 280 MGSO4, PH 5.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 27.22133 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 54.44267 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 40.83200 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 68.05333 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 13.61067 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4750 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21480 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -58.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, T, P 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 -6 REMARK 465 ALA A -5 REMARK 465 HIS A -4 REMARK 465 HIS A -3 REMARK 465 HIS A -2 REMARK 465 HIS A -1 REMARK 465 HIS A 0 REMARK 465 HIS A 1 REMARK 465 THR A 155 REMARK 465 THR A 156 REMARK 465 ALA A 157 REMARK 465 GLU A 158 REMARK 465 GLU A 159 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 DC T 1 O5' C5' C4' O4' C3' C2' C1' REMARK 470 DC T 1 N1 C2 O2 N3 C4 N4 C5 REMARK 470 DC T 1 C6 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 SER A 213 CA CB OG REMARK 480 SER A 288 OG 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 HE ARG A 256 O HOH A 612 1.48 REMARK 500 HH21 ARG A 128 O HOH A 609 1.49 REMARK 500 HE21 GLN A 249 O HOH A 615 1.56 REMARK 500 O HOH A 815 O HOH A 835 1.85 REMARK 500 O HOH A 624 O HOH A 865 1.91 REMARK 500 O HOH T 112 O HOH T 138 2.00 REMARK 500 O HOH A 675 O HOH A 701 2.01 REMARK 500 O HOH A 615 O HOH A 740 2.06 REMARK 500 OE1 GLU A 94 O HOH A 601 2.10 REMARK 500 O HOH A 825 O HOH A 884 2.13 REMARK 500 O HOH A 653 O HOH A 814 2.13 REMARK 500 OE1 GLN A 79 O HOH A 602 2.14 REMARK 500 O HOH T 111 O HOH P 203 2.17 REMARK 500 OE1 GLN A 189 O HOH A 603 2.17 REMARK 500 O HOH A 842 O HOH A 878 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 862 O HOH A 866 6665 1.95 REMARK 500 O HOH A 716 O HOH A 852 6555 2.00 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 DI T 4 C2' DI T 4 C1' -0.181 REMARK 500 DI T 4 O4' DI T 4 C1' 0.182 REMARK 500 DI T 4 C5 DI T 4 C6 0.139 REMARK 500 DT T 12 C5 DT T 12 C7 -0.050 REMARK 500 DT P 5 C5 DT P 5 C7 -0.045 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 256 NE - CZ - NH2 ANGL. DEV. = 3.9 DEGREES REMARK 500 DT T 3 O4' - C1' - C2' ANGL. DEV. = 4.0 DEGREES REMARK 500 DG T 7 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 DC T 9 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 DT T 12 O4' - C1' - N1 ANGL. DEV. = 1.9 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 CYS A 16 63.36 24.60 REMARK 500 TYR A 39 -175.66 70.98 REMARK 500 LYS A 40 -40.21 -152.85 REMARK 500 SER A 62 -14.91 79.78 REMARK 500 SER A 217 -156.30 -155.28 REMARK 500 SER A 257 -8.84 94.46 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 MG A 502 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 13 OD1 REMARK 620 2 MET A 14 O 83.4 REMARK 620 3 ASP A 115 OD2 95.4 85.4 REMARK 620 4 0KX A 501 O2G 82.6 94.2 178.0 REMARK 620 5 0KX A 501 O2B 165.5 89.8 96.7 85.2 REMARK 620 6 0KX A 501 O1A 101.6 172.8 89.0 91.6 86.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 503 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 13 OD2 REMARK 620 2 ASP A 115 OD1 94.9 REMARK 620 3 GLU A 116 OE2 87.5 91.6 REMARK 620 4 0KX A 501 O1A 100.2 88.8 172.1 REMARK 620 5 HOH A 715 O 90.5 168.0 99.3 79.8 REMARK 620 6 DT P 8 O3' 166.8 91.7 80.8 91.3 85.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 504 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 358 O REMARK 620 2 HOH A 876 O 133.2 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA P 101 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 896 O REMARK 620 2 DT P 8 OP2 149.4 REMARK 620 3 DT P 8 O5' 127.9 66.9 REMARK 620 4 HOH P 207 O 91.6 64.4 75.6 REMARK 620 5 HOH P 221 O 67.3 108.4 158.5 122.4 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 0KX A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA P 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6MP3 RELATED DB: PDB REMARK 900 SAME PROTEIN-DNA COMPLEX, BUT WITH NO INCOMING NUCLEOTIDE DBREF 6MQ8 A 3 432 UNP Q9Y253 POLH_HUMAN 3 432 DBREF 6MQ8 T 1 12 PDB 6MQ8 6MQ8 1 12 DBREF 6MQ8 P 1 8 PDB 6MQ8 6MQ8 1 8 SEQADV 6MQ8 MET A -6 UNP Q9Y253 INITIATING METHIONINE SEQADV 6MQ8 ALA A -5 UNP Q9Y253 EXPRESSION TAG SEQADV 6MQ8 HIS A -4 UNP Q9Y253 EXPRESSION TAG SEQADV 6MQ8 HIS A -3 UNP Q9Y253 EXPRESSION TAG SEQADV 6MQ8 HIS A -2 UNP Q9Y253 EXPRESSION TAG SEQADV 6MQ8 HIS A -1 UNP Q9Y253 EXPRESSION TAG SEQADV 6MQ8 HIS A 0 UNP Q9Y253 EXPRESSION TAG SEQADV 6MQ8 HIS A 1 UNP Q9Y253 EXPRESSION TAG SEQADV 6MQ8 GLY A 2 UNP Q9Y253 EXPRESSION TAG SEQRES 1 A 439 MET ALA HIS HIS HIS HIS HIS HIS GLY THR GLY GLN ASP SEQRES 2 A 439 ARG VAL VAL ALA LEU VAL ASP MET ASP CYS PHE PHE VAL SEQRES 3 A 439 GLN VAL GLU GLN ARG GLN ASN PRO HIS LEU ARG ASN LYS SEQRES 4 A 439 PRO CYS ALA VAL VAL GLN TYR LYS SER TRP LYS GLY GLY SEQRES 5 A 439 GLY ILE ILE ALA VAL SER TYR GLU ALA ARG ALA PHE GLY SEQRES 6 A 439 VAL THR ARG SER MET TRP ALA ASP ASP ALA LYS LYS LEU SEQRES 7 A 439 CYS PRO ASP LEU LEU LEU ALA GLN VAL ARG GLU SER ARG SEQRES 8 A 439 GLY LYS ALA ASN LEU THR LYS TYR ARG GLU ALA SER VAL SEQRES 9 A 439 GLU VAL MET GLU ILE MET SER ARG PHE ALA VAL ILE GLU SEQRES 10 A 439 ARG ALA SER ILE ASP GLU ALA TYR VAL ASP LEU THR SER SEQRES 11 A 439 ALA VAL GLN GLU ARG LEU GLN LYS LEU GLN GLY GLN PRO SEQRES 12 A 439 ILE SER ALA ASP LEU LEU PRO SER THR TYR ILE GLU GLY SEQRES 13 A 439 LEU PRO GLN GLY PRO THR THR ALA GLU GLU THR VAL GLN SEQRES 14 A 439 LYS GLU GLY MET ARG LYS GLN GLY LEU PHE GLN TRP LEU SEQRES 15 A 439 ASP SER LEU GLN ILE ASP ASN LEU THR SER PRO ASP LEU SEQRES 16 A 439 GLN LEU THR VAL GLY ALA VAL ILE VAL GLU GLU MET ARG SEQRES 17 A 439 ALA ALA ILE GLU ARG GLU THR GLY PHE GLN CYS SER ALA SEQRES 18 A 439 GLY ILE SER HIS ASN LYS VAL LEU ALA LYS LEU ALA CYS SEQRES 19 A 439 GLY LEU ASN LYS PRO ASN ARG GLN THR LEU VAL SER HIS SEQRES 20 A 439 GLY SER VAL PRO GLN LEU PHE SER GLN MET PRO ILE ARG SEQRES 21 A 439 LYS ILE ARG SER LEU GLY GLY LYS LEU GLY ALA SER VAL SEQRES 22 A 439 ILE GLU ILE LEU GLY ILE GLU TYR MET GLY GLU LEU THR SEQRES 23 A 439 GLN PHE THR GLU SER GLN LEU GLN SER HIS PHE GLY GLU SEQRES 24 A 439 LYS ASN GLY SER TRP LEU TYR ALA MET CYS ARG GLY ILE SEQRES 25 A 439 GLU HIS ASP PRO VAL LYS PRO ARG GLN LEU PRO LYS THR SEQRES 26 A 439 ILE GLY CYS SER LYS ASN PHE PRO GLY LYS THR ALA LEU SEQRES 27 A 439 ALA THR ARG GLU GLN VAL GLN TRP TRP LEU LEU GLN LEU SEQRES 28 A 439 ALA GLN GLU LEU GLU GLU ARG LEU THR LYS ASP ARG ASN SEQRES 29 A 439 ASP ASN ASP ARG VAL ALA THR GLN LEU VAL VAL SER ILE SEQRES 30 A 439 ARG VAL GLN GLY ASP LYS ARG LEU SER SER LEU ARG ARG SEQRES 31 A 439 CYS CYS ALA LEU THR ARG TYR ASP ALA HIS LYS MET SER SEQRES 32 A 439 HIS ASP ALA PHE THR VAL ILE LYS ASN CYS ASN THR SER SEQRES 33 A 439 GLY ILE GLN THR GLU TRP SER PRO PRO LEU THR MET LEU SEQRES 34 A 439 PHE LEU CYS ALA THR LYS PHE SER ALA SER SEQRES 1 T 12 DC DA DT DI DA DT DG DA DC DG DC DT SEQRES 1 P 8 DA DG DC DG DT DC DA DT HET 0KX A 501 41 HET MG A 502 1 HET MG A 503 1 HET NA A 504 1 HET NA P 101 1 HETNAM 0KX 2'-DEOXY-5'-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY) HETNAM 2 0KX PHOSPHORYL]AMINO}PHOSPHORYL]CYTIDINE HETNAM MG MAGNESIUM ION HETNAM NA SODIUM ION FORMUL 4 0KX C9 H17 N4 O12 P3 FORMUL 5 MG 2(MG 2+) FORMUL 7 NA 2(NA 1+) FORMUL 9 HOH *365(H2 O) HELIX 1 AA1 CYS A 16 ASN A 26 1 11 HELIX 2 AA2 PRO A 27 ARG A 30 5 4 HELIX 3 AA3 SER A 51 ALA A 56 1 6 HELIX 4 AA4 TRP A 64 CYS A 72 1 9 HELIX 5 AA5 LEU A 89 ARG A 105 1 17 HELIX 6 AA6 LEU A 121 LEU A 132 1 12 HELIX 7 AA7 SER A 138 LEU A 142 5 5 HELIX 8 AA8 GLN A 162 SER A 177 1 16 HELIX 9 AA9 SER A 185 GLY A 209 1 25 HELIX 10 AB1 ASN A 219 ASN A 230 1 12 HELIX 11 AB2 SER A 239 GLY A 241 5 3 HELIX 12 AB3 SER A 242 GLN A 249 1 8 HELIX 13 AB4 MET A 250 ILE A 255 5 6 HELIX 14 AB5 GLY A 260 GLY A 271 1 12 HELIX 15 AB6 TYR A 274 PHE A 281 5 8 HELIX 16 AB7 THR A 282 GLY A 291 1 10 HELIX 17 AB8 GLY A 291 CYS A 302 1 12 HELIX 18 AB9 PRO A 326 ALA A 330 5 5 HELIX 19 AC1 ARG A 334 ASP A 360 1 27 HELIX 20 AC2 ASP A 391 LYS A 404 1 14 HELIX 21 AC3 ASN A 405 ASN A 407 5 3 SHEET 1 AA1 6 ILE A 109 SER A 113 0 SHEET 2 AA1 6 GLU A 116 ASP A 120 -1 O TYR A 118 N GLU A 110 SHEET 3 AA1 6 VAL A 9 MET A 14 -1 N ALA A 10 O VAL A 119 SHEET 4 AA1 6 CYS A 212 SER A 217 -1 O SER A 217 N VAL A 9 SHEET 5 AA1 6 GLN A 235 LEU A 237 1 O THR A 236 N ILE A 216 SHEET 6 AA1 6 THR A 145 ILE A 147 1 N TYR A 146 O LEU A 237 SHEET 1 AA2 3 GLY A 46 VAL A 50 0 SHEET 2 AA2 3 CYS A 34 GLN A 38 -1 N VAL A 36 O ILE A 48 SHEET 3 AA2 3 LEU A 76 GLN A 79 1 O ALA A 78 N VAL A 37 SHEET 1 AA3 2 GLU A 82 SER A 83 0 SHEET 2 AA3 2 LYS A 86 ALA A 87 -1 O LYS A 86 N SER A 83 SHEET 1 AA4 3 ILE A 319 ASN A 324 0 SHEET 2 AA4 3 GLU A 414 ALA A 431 -1 O ALA A 426 N ILE A 319 SHEET 3 AA4 3 LEU A 331 THR A 333 -1 N ALA A 332 O TRP A 415 SHEET 1 AA5 4 ILE A 319 ASN A 324 0 SHEET 2 AA5 4 GLU A 414 ALA A 431 -1 O ALA A 426 N ILE A 319 SHEET 3 AA5 4 ARG A 361 VAL A 372 -1 N VAL A 367 O CYS A 425 SHEET 4 AA5 4 LEU A 381 ALA A 386 -1 O ARG A 383 N VAL A 368 LINK OD1 ASP A 13 MG MG A 502 1555 1555 2.00 LINK OD2 ASP A 13 MG MG A 503 1555 1555 1.99 LINK O MET A 14 MG MG A 502 1555 1555 2.16 LINK OD2 ASP A 115 MG MG A 502 1555 1555 2.02 LINK OD1 ASP A 115 MG MG A 503 1555 1555 2.10 LINK OE2 GLU A 116 MG MG A 503 1555 1555 2.07 LINK O ASP A 358 NA NA A 504 1555 1555 2.91 LINK O2G 0KX A 501 MG MG A 502 1555 1555 2.12 LINK O2B 0KX A 501 MG MG A 502 1555 1555 2.06 LINK O1A 0KX A 501 MG MG A 502 1555 1555 2.04 LINK O1A 0KX A 501 MG MG A 503 1555 1555 2.23 LINK MG MG A 503 O HOH A 715 1555 1555 2.17 LINK MG MG A 503 O3' DT P 8 1555 1555 2.16 LINK NA NA A 504 O HOH A 876 1555 1555 2.44 LINK O HOH A 896 NA NA P 101 1555 1555 2.84 LINK OP2 DT P 8 NA NA P 101 1555 1555 2.10 LINK O5' DT P 8 NA NA P 101 1555 1555 2.43 LINK NA NA P 101 O HOH P 207 1555 1555 2.83 LINK NA NA P 101 O HOH P 221 1555 1555 2.15 CISPEP 1 LEU A 150 PRO A 151 0 1.44 CISPEP 2 LYS A 231 PRO A 232 0 -1.94 CISPEP 3 SER A 416 PRO A 417 0 -3.76 SITE 1 AC1 24 ASP A 13 MET A 14 ASP A 15 CYS A 16 SITE 2 AC1 24 PHE A 17 PHE A 18 ILE A 48 ALA A 49 SITE 3 AC1 24 TYR A 52 ARG A 55 ARG A 61 ASP A 115 SITE 4 AC1 24 LYS A 231 MG A 502 MG A 503 HOH A 619 SITE 5 AC1 24 HOH A 641 HOH A 643 HOH A 682 HOH A 715 SITE 6 AC1 24 HOH A 729 HOH A 746 DT P 8 DI T 4 SITE 1 AC2 5 ASP A 13 MET A 14 ASP A 115 0KX A 501 SITE 2 AC2 5 MG A 503 SITE 1 AC3 7 ASP A 13 ASP A 115 GLU A 116 0KX A 501 SITE 2 AC3 7 MG A 502 HOH A 715 DT P 8 SITE 1 AC4 2 ASP A 358 HOH A 876 SITE 1 AC5 5 HOH A 896 DA P 7 DT P 8 HOH P 207 SITE 2 AC5 5 HOH P 221 CRYST1 98.539 98.539 81.664 90.00 90.00 120.00 P 61 6 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 0.010148 0.005859 0.000000 0.00000 SCALE2 0.000000 0.011718 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012245 0.00000