HEADER TRANSFERASE/DNA 18-DEC-13 4O3N TITLE CRYSTAL STRUCTURE OF HUMAN DNA POLYMERASE ETA IN TERNARY COMPLEX WITH TITLE 2 NATIVE DNA AND INCOMING NUCLEOTIDE (DCP) 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*GP*AP*TP*GP*AP*CP*GP*CP*T)-3'); COMPND 9 CHAIN: T; COMPND 10 ENGINEERED: YES; COMPND 11 OTHER_DETAILS: NUCLEIC ACIDS TEMPLATE: CAT GAT GAC GCT; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: DNA (5'-D(*AP*GP*CP*GP*TP*CP*AP*T)-3'); COMPND 14 CHAIN: P; COMPND 15 ENGINEERED: YES; COMPND 16 OTHER_DETAILS: NUCLEIC ACIDS PRIMAR: AGCGTCAT 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; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 OTHER_DETAILS: CHEMICALLY SYNTHESIZED; SOURCE 11 MOL_ID: 3; SOURCE 12 SYNTHETIC: YES; SOURCE 13 OTHER_DETAILS: CHEMICALLY SYNTHESIZED KEYWDS CATALYTIC DOMAIN, DNA, DNA DAMAGE, DNA-DIRECTED DNA POLYMERASE, KEYWDS 2 CYTOSINE TRIPHOSPHATE, Y-FAMILY POLYMERASE, TRANS-LESION SYNTHESIS KEYWDS 3 (TLS), DNA BINDING, TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR A.PATRA,M.EGLI REVDAT 3 20-SEP-23 4O3N 1 REMARK SEQADV LINK REVDAT 2 02-JUL-14 4O3N 1 JRNL REVDAT 1 30-APR-14 4O3N 0 JRNL AUTH A.PATRA,L.D.NAGY,Q.ZHANG,Y.SU,L.MULLER,F.P.GUENGERICH,M.EGLI JRNL TITL KINETICS, STRUCTURE, AND MECHANISM OF JRNL TITL 2 8-OXO-7,8-DIHYDRO-2'-DEOXYGUANOSINE BYPASS BY HUMAN DNA JRNL TITL 3 POLYMERASE ETA JRNL REF J.BIOL.CHEM. V. 289 16867 2014 JRNL REFN ISSN 0021-9258 JRNL PMID 24759104 JRNL DOI 10.1074/JBC.M114.551820 REMARK 2 REMARK 2 RESOLUTION. 1.58 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: DEV_1516) 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) : 1.58 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.24 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 61922 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.172 REMARK 3 R VALUE (WORKING SET) : 0.170 REMARK 3 FREE R VALUE : 0.215 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.070 REMARK 3 FREE R VALUE TEST SET COUNT : 3138 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 42.2570 - 4.4238 0.99 2721 138 0.1770 0.2518 REMARK 3 2 4.4238 - 3.5118 1.00 2677 155 0.1441 0.1796 REMARK 3 3 3.5118 - 3.0680 1.00 2700 147 0.1552 0.1938 REMARK 3 4 3.0680 - 2.7876 1.00 2665 151 0.1722 0.1854 REMARK 3 5 2.7876 - 2.5878 1.00 2692 139 0.1714 0.2160 REMARK 3 6 2.5878 - 2.4353 1.00 2680 147 0.1827 0.2394 REMARK 3 7 2.4353 - 2.3133 1.00 2646 165 0.1639 0.1993 REMARK 3 8 2.3133 - 2.2126 1.00 2662 143 0.1652 0.2323 REMARK 3 9 2.2126 - 2.1274 1.00 2679 141 0.1684 0.2185 REMARK 3 10 2.1274 - 2.0540 1.00 2648 150 0.1757 0.2343 REMARK 3 11 2.0540 - 1.9898 1.00 2706 125 0.1757 0.2206 REMARK 3 12 1.9898 - 1.9329 1.00 2673 127 0.1722 0.1996 REMARK 3 13 1.9329 - 1.8820 1.00 2706 124 0.1748 0.2004 REMARK 3 14 1.8820 - 1.8361 1.00 2648 136 0.1728 0.2424 REMARK 3 15 1.8361 - 1.7944 1.00 2674 153 0.1762 0.2294 REMARK 3 16 1.7944 - 1.7562 1.00 2653 136 0.1779 0.2292 REMARK 3 17 1.7562 - 1.7211 1.00 2652 140 0.1824 0.2337 REMARK 3 18 1.7211 - 1.6886 1.00 2677 140 0.1917 0.2324 REMARK 3 19 1.6886 - 1.6584 1.00 2659 160 0.2039 0.2507 REMARK 3 20 1.6584 - 1.6303 1.00 2654 149 0.2065 0.2291 REMARK 3 21 1.6303 - 1.6040 1.00 2646 145 0.2344 0.2808 REMARK 3 22 1.6040 - 1.5793 1.00 2666 127 0.2382 0.2556 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) : 21.230 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.019 4022 REMARK 3 ANGLE : 1.816 5534 REMARK 3 CHIRALITY : 0.090 615 REMARK 3 PLANARITY : 0.010 644 REMARK 3 DIHEDRAL : 20.189 1588 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 4O3N COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-JAN-14. REMARK 100 THE DEPOSITION ID IS D_1000084000. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-AUG-13 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 : 21-ID-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.07810 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 61922 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.579 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 7.400 REMARK 200 R MERGE (I) : 0.06500 REMARK 200 R SYM (I) : 0.06500 REMARK 200 FOR THE DATA SET : 37.3970 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.58 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.61 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 7.10 REMARK 200 R MERGE FOR SHELL (I) : 0.90000 REMARK 200 R SYM FOR SHELL (I) : 0.90000 REMARK 200 FOR SHELL : 2.204 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER (MR) REMARK 200 STARTING MODEL: PDB ENTRY 4ECQ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.44 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M MES PH 5.5, 5MM MAGNESIUM REMARK 280 CHLORIDE, 15.5% PEG 2000 MME, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 291.0K 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 27.26233 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 54.52467 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 40.89350 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 68.15583 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 13.63117 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: 4670 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21920 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -44.0 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 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 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 O HOH A 787 O HOH A 977 1.68 REMARK 500 O HOH A 759 O HOH A 977 1.80 REMARK 500 O HOH A 773 O HOH A 871 1.85 REMARK 500 O HOH A 957 O HOH A 989 1.88 REMARK 500 O HOH A 614 O HOH A 958 1.97 REMARK 500 O HOH A 722 O HOH A 974 2.00 REMARK 500 O HOH A 817 O HOH A 958 2.00 REMARK 500 O HOH A 822 O HOH A 876 2.01 REMARK 500 O HOH T 101 O HOH T 102 2.02 REMARK 500 O HOH A 984 O HOH A 992 2.03 REMARK 500 NH2 ARG A 256 O HOH A 733 2.04 REMARK 500 O HOH A 810 O HOH A 927 2.05 REMARK 500 O HOH A 889 O HOH A 890 2.06 REMARK 500 O HOH A 771 O HOH A 772 2.08 REMARK 500 O HOH A 680 O HOH A 973 2.09 REMARK 500 O HOH A 938 O HOH A 993 2.10 REMARK 500 O HOH P 111 O HOH P 119 2.13 REMARK 500 O HOH A 874 O HOH A 972 2.13 REMARK 500 O HOH A 972 O HOH A 975 2.13 REMARK 500 O HOH A 874 O HOH A 975 2.14 REMARK 500 O HOH A 945 O HOH A 946 2.14 REMARK 500 O HOH A 873 O HOH A 919 2.16 REMARK 500 NH2 ARG A 256 O HOH A 734 2.19 REMARK 500 OP1 DT P 8 O HOH P 124 2.19 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 849 O HOH A 856 6765 2.13 REMARK 500 O HOH A 871 O HOH A 954 6865 2.18 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 CYS A 384 CB CYS A 384 SG -0.102 REMARK 500 DT T 6 O3' DT T 6 C3' -0.039 REMARK 500 DG T 7 O3' DG T 7 C3' -0.052 REMARK 500 DG P 2 O3' DG P 2 C3' -0.081 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 167 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG A 206 NE - CZ - NH1 ANGL. DEV. = -5.0 DEGREES REMARK 500 ARG A 206 NE - CZ - NH2 ANGL. DEV. = 4.3 DEGREES REMARK 500 ARG A 351 NE - CZ - NH2 ANGL. DEV. = -4.0 DEGREES REMARK 500 DG T 4 OP1 - P - OP2 ANGL. DEV. = 9.3 DEGREES REMARK 500 DC T 9 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 DT T 12 O4' - C1' - N1 ANGL. DEV. = 5.2 DEGREES REMARK 500 DG P 2 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 DC P 3 O3' - P - OP2 ANGL. DEV. = 7.2 DEGREES REMARK 500 DA P 7 O4' - C4' - C3' ANGL. DEV. = -5.0 DEGREES REMARK 500 DA P 7 C3' - O3' - P ANGL. DEV. = 8.2 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 64.09 25.34 REMARK 500 TYR A 39 80.80 63.06 REMARK 500 SER A 62 -8.48 77.13 REMARK 500 GLN A 133 -70.40 62.15 REMARK 500 SER A 217 -157.40 -155.56 REMARK 500 SER A 257 -11.62 97.08 REMARK 500 LEU A 381 129.74 -171.95 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 OD2 REMARK 620 2 MET A 14 O 83.5 REMARK 620 3 ASP A 115 OD2 97.4 85.7 REMARK 620 4 0KX A 501 O1B 167.3 88.0 91.3 REMARK 620 5 0KX A 501 O1G 85.9 93.6 176.5 85.3 REMARK 620 6 0KX A 501 O2A 100.4 173.8 89.0 88.9 91.5 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 OD1 REMARK 620 2 ASP A 115 OD1 96.2 REMARK 620 3 GLU A 116 OE1 86.1 94.5 REMARK 620 4 0KX A 501 O2A 102.0 89.6 170.5 REMARK 620 5 HOH A 603 O 87.7 166.2 98.9 76.6 REMARK 620 6 DT P 8 O3' 167.8 89.9 82.9 88.5 88.8 REMARK 620 7 DT P 8 O3' 168.1 81.3 82.5 89.7 97.4 8.6 REMARK 620 N 1 2 3 4 5 6 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 GOL A 504 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4O3O RELATED DB: PDB REMARK 900 RELATED ID: 4O3P RELATED DB: PDB REMARK 900 RELATED ID: 4O3Q RELATED DB: PDB REMARK 900 RELATED ID: 4O3R RELATED DB: PDB REMARK 900 RELATED ID: 4O3S RELATED DB: PDB DBREF 4O3N A 1 432 UNP Q9Y253 POLH_HUMAN 1 432 DBREF 4O3N T 1 12 PDB 4O3N 4O3N 1 12 DBREF 4O3N P 1 8 PDB 4O3N 4O3N 1 8 SEQADV 4O3N GLY A -2 UNP Q9Y253 EXPRESSION TAG SEQADV 4O3N PRO A -1 UNP Q9Y253 EXPRESSION TAG SEQADV 4O3N HIS A 0 UNP Q9Y253 EXPRESSION TAG SEQRES 1 A 435 GLY PRO HIS MET ALA THR GLY GLN ASP ARG VAL VAL ALA SEQRES 2 A 435 LEU VAL ASP MET ASP CYS PHE PHE VAL GLN VAL GLU GLN SEQRES 3 A 435 ARG GLN ASN PRO HIS LEU ARG ASN LYS PRO CYS ALA VAL SEQRES 4 A 435 VAL GLN TYR LYS SER TRP LYS GLY GLY GLY ILE ILE ALA SEQRES 5 A 435 VAL SER TYR GLU ALA ARG ALA PHE GLY VAL THR ARG SER SEQRES 6 A 435 MET TRP ALA ASP ASP ALA LYS LYS LEU CYS PRO ASP LEU SEQRES 7 A 435 LEU LEU ALA GLN VAL ARG GLU SER ARG GLY LYS ALA ASN SEQRES 8 A 435 LEU THR LYS TYR ARG GLU ALA SER VAL GLU VAL MET GLU SEQRES 9 A 435 ILE MET SER ARG PHE ALA VAL ILE GLU ARG ALA SER ILE SEQRES 10 A 435 ASP GLU ALA TYR VAL ASP LEU THR SER ALA VAL GLN GLU SEQRES 11 A 435 ARG LEU GLN LYS LEU GLN GLY GLN PRO ILE SER ALA ASP SEQRES 12 A 435 LEU LEU PRO SER THR TYR ILE GLU GLY LEU PRO GLN GLY SEQRES 13 A 435 PRO THR THR ALA GLU GLU THR VAL GLN LYS GLU GLY MET SEQRES 14 A 435 ARG LYS GLN GLY LEU PHE GLN TRP LEU ASP SER LEU GLN SEQRES 15 A 435 ILE ASP ASN LEU THR SER PRO ASP LEU GLN LEU THR VAL SEQRES 16 A 435 GLY ALA VAL ILE VAL GLU GLU MET ARG ALA ALA ILE GLU SEQRES 17 A 435 ARG GLU THR GLY PHE GLN CYS SER ALA GLY ILE SER HIS SEQRES 18 A 435 ASN LYS VAL LEU ALA LYS LEU ALA CYS GLY LEU ASN LYS SEQRES 19 A 435 PRO ASN ARG GLN THR LEU VAL SER HIS GLY SER VAL PRO SEQRES 20 A 435 GLN LEU PHE SER GLN MET PRO ILE ARG LYS ILE ARG SER SEQRES 21 A 435 LEU GLY GLY LYS LEU GLY ALA SER VAL ILE GLU ILE LEU SEQRES 22 A 435 GLY ILE GLU TYR MET GLY GLU LEU THR GLN PHE THR GLU SEQRES 23 A 435 SER GLN LEU GLN SER HIS PHE GLY GLU LYS ASN GLY SER SEQRES 24 A 435 TRP LEU TYR ALA MET CYS ARG GLY ILE GLU HIS ASP PRO SEQRES 25 A 435 VAL LYS PRO ARG GLN LEU PRO LYS THR ILE GLY CYS SER SEQRES 26 A 435 LYS ASN PHE PRO GLY LYS THR ALA LEU ALA THR ARG GLU SEQRES 27 A 435 GLN VAL GLN TRP TRP LEU LEU GLN LEU ALA GLN GLU LEU SEQRES 28 A 435 GLU GLU ARG LEU THR LYS ASP ARG ASN ASP ASN ASP ARG SEQRES 29 A 435 VAL ALA THR GLN LEU VAL VAL SER ILE ARG VAL GLN GLY SEQRES 30 A 435 ASP LYS ARG LEU SER SER LEU ARG ARG CYS CYS ALA LEU SEQRES 31 A 435 THR ARG TYR ASP ALA HIS LYS MET SER HIS ASP ALA PHE SEQRES 32 A 435 THR VAL ILE LYS ASN CYS ASN THR SER GLY ILE GLN THR SEQRES 33 A 435 GLU TRP SER PRO PRO LEU THR MET LEU PHE LEU CYS ALA SEQRES 34 A 435 THR LYS PHE SER ALA SER SEQRES 1 T 12 DC DA DT DG DA DT DG DA DC DG DC DT SEQRES 1 P 8 DA DG DC DG DT DC DA DT HET 0KX A 501 28 HET MG A 502 1 HET MG A 503 1 HET GOL A 504 6 HETNAM 0KX 2'-DEOXY-5'-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY) HETNAM 2 0KX PHOSPHORYL]AMINO}PHOSPHORYL]CYTIDINE HETNAM MG MAGNESIUM ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 4 0KX C9 H17 N4 O12 P3 FORMUL 5 MG 2(MG 2+) FORMUL 7 GOL C3 H8 O3 FORMUL 8 HOH *475(H2 O) HELIX 1 1 CYS A 16 ASN A 26 1 11 HELIX 2 2 PRO A 27 ARG A 30 5 4 HELIX 3 3 SER A 51 ALA A 56 1 6 HELIX 4 4 TRP A 64 CYS A 72 1 9 HELIX 5 5 LEU A 89 ALA A 107 1 19 HELIX 6 6 LEU A 121 LEU A 132 1 12 HELIX 7 7 SER A 138 LEU A 142 5 5 HELIX 8 8 GLN A 162 SER A 177 1 16 HELIX 9 9 SER A 185 GLY A 209 1 25 HELIX 10 10 ASN A 219 ASN A 230 1 12 HELIX 11 11 SER A 242 GLN A 249 1 8 HELIX 12 12 MET A 250 ILE A 255 5 6 HELIX 13 13 GLY A 260 GLY A 271 1 12 HELIX 14 14 TYR A 274 PHE A 281 5 8 HELIX 15 15 THR A 282 GLY A 291 1 10 HELIX 16 16 GLY A 291 CYS A 302 1 12 HELIX 17 17 PRO A 326 ALA A 330 5 5 HELIX 18 18 ARG A 334 ASP A 360 1 27 HELIX 19 19 ASP A 391 LYS A 404 1 14 SHEET 1 A 6 ILE A 109 SER A 113 0 SHEET 2 A 6 GLU A 116 ASP A 120 -1 O TYR A 118 N GLU A 110 SHEET 3 A 6 VAL A 9 MET A 14 -1 N VAL A 12 O ALA A 117 SHEET 4 A 6 CYS A 212 SER A 217 -1 O SER A 217 N VAL A 9 SHEET 5 A 6 GLN A 235 LEU A 237 1 O THR A 236 N ILE A 216 SHEET 6 A 6 THR A 145 ILE A 147 1 N TYR A 146 O LEU A 237 SHEET 1 B 3 GLY A 46 VAL A 50 0 SHEET 2 B 3 CYS A 34 GLN A 38 -1 N VAL A 36 O ILE A 48 SHEET 3 B 3 LEU A 76 GLN A 79 1 O ALA A 78 N VAL A 37 SHEET 1 C 2 GLU A 82 SER A 83 0 SHEET 2 C 2 LYS A 86 ALA A 87 -1 O LYS A 86 N SER A 83 SHEET 1 D 3 ILE A 319 ASN A 324 0 SHEET 2 D 3 GLU A 414 ALA A 431 -1 O ALA A 426 N ILE A 319 SHEET 3 D 3 LEU A 331 THR A 333 -1 N ALA A 332 O TRP A 415 SHEET 1 E 4 ILE A 319 ASN A 324 0 SHEET 2 E 4 GLU A 414 ALA A 431 -1 O ALA A 426 N ILE A 319 SHEET 3 E 4 ARG A 361 VAL A 372 -1 N VAL A 367 O CYS A 425 SHEET 4 E 4 LEU A 381 ALA A 386 -1 O ARG A 383 N VAL A 368 LINK OD2 ASP A 13 MG MG A 502 1555 1555 2.05 LINK OD1 ASP A 13 MG MG A 503 1555 1555 2.04 LINK O MET A 14 MG MG A 502 1555 1555 2.21 LINK OD2 ASP A 115 MG MG A 502 1555 1555 2.12 LINK OD1 ASP A 115 MG MG A 503 1555 1555 2.16 LINK OE1 GLU A 116 MG MG A 503 1555 1555 2.06 LINK O1B 0KX A 501 MG MG A 502 1555 1555 2.15 LINK O1G 0KX A 501 MG MG A 502 1555 1555 2.17 LINK O2A 0KX A 501 MG MG A 502 1555 1555 2.23 LINK O2A 0KX A 501 MG MG A 503 1555 1555 2.23 LINK MG MG A 503 O HOH A 603 1555 1555 2.16 LINK MG MG A 503 O3'B DT P 8 1555 1555 2.05 LINK MG MG A 503 O3'A DT P 8 1555 1555 2.44 CISPEP 1 LEU A 150 PRO A 151 0 2.32 CISPEP 2 LYS A 231 PRO A 232 0 5.40 CISPEP 3 SER A 416 PRO A 417 0 -8.72 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 603 SITE 5 AC1 24 HOH A 604 HOH A 606 HOH A 609 HOH A 619 SITE 6 AC1 24 HOH A 832 DT P 8 HOH P 102 DG 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 603 DT P 8 SITE 1 AC4 8 PRO A 244 PHE A 247 SER A 248 GLY A 276 SITE 2 AC4 8 GLU A 277 HOH A 999 HOH A1000 HOH A1001 CRYST1 98.662 98.662 81.787 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 0.010136 0.005852 0.000000 0.00000 SCALE2 0.000000 0.011704 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012227 0.00000