HEADER TRANSFERASE/DNA 26-MAR-12 4ECV TITLE HUMAN DNA POLYMERASE ETA - DNA TERNARY COMPLEX: REACTION IN THE AT TITLE 2 CRYSTAL AT PH 7.0 FOR 230 SEC COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE ETA; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CATALYTIC CORE (UNP RESIDUES 1-432); COMPND 5 SYNONYM: RAD30 HOMOLOG A, XERODERMA PIGMENTOSUM VARIANT TYPE PROTEIN; COMPND 6 EC: 2.7.7.7; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: DNA (5'-D(*CP*AP*TP*TP*AP*TP*GP*AP*CP*GP*CP*T)-3'); COMPND 10 CHAIN: T; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: DNA (5'-D(*AP*GP*CP*GP*TP*CP*AP*TP*A)-3'); COMPND 14 CHAIN: P; COMPND 15 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; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)PLYSS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 MOL_ID: 3; SOURCE 14 SYNTHETIC: YES KEYWDS TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR T.NAKAMURA,Y.ZHAO,W.YANG REVDAT 3 20-MAR-24 4ECV 1 REMARK SEQADV LINK REVDAT 2 25-JUL-12 4ECV 1 JRNL REVDAT 1 11-JUL-12 4ECV 0 JRNL AUTH T.NAKAMURA,Y.ZHAO,Y.YAMAGATA,Y.J.HUA,W.YANG JRNL TITL WATCHING DNA POLYMERASE ETA MAKE A PHOSPHODIESTER BOND JRNL REF NATURE V. 487 196 2012 JRNL REFN ISSN 0028-0836 JRNL PMID 22785315 JRNL DOI 10.1038/NATURE11181 REMARK 2 REMARK 2 RESOLUTION. 1.52 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.6.1_357) 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) : 1.52 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.01 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.390 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 69345 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.174 REMARK 3 R VALUE (WORKING SET) : 0.173 REMARK 3 FREE R VALUE : 0.205 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.050 REMARK 3 FREE R VALUE TEST SET COUNT : 3499 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 24.0147 - 4.4382 0.94 2544 153 0.1701 0.1758 REMARK 3 2 4.4382 - 3.5263 0.99 2643 156 0.1413 0.1668 REMARK 3 3 3.5263 - 3.0816 1.00 2675 136 0.1537 0.1901 REMARK 3 4 3.0816 - 2.8003 1.00 2663 144 0.1750 0.2152 REMARK 3 5 2.8003 - 2.5998 1.00 2666 140 0.1785 0.1995 REMARK 3 6 2.5998 - 2.4467 1.00 2680 127 0.1771 0.2341 REMARK 3 7 2.4467 - 2.3243 1.00 2672 129 0.1670 0.1952 REMARK 3 8 2.3243 - 2.2232 1.00 2640 146 0.1561 0.2084 REMARK 3 9 2.2232 - 2.1376 1.00 2662 131 0.1555 0.1909 REMARK 3 10 2.1376 - 2.0639 1.00 2647 133 0.1587 0.1693 REMARK 3 11 2.0639 - 1.9994 1.00 2679 132 0.1649 0.2257 REMARK 3 12 1.9994 - 1.9423 1.00 2621 156 0.1603 0.2121 REMARK 3 13 1.9423 - 1.8912 1.00 2651 160 0.1673 0.1939 REMARK 3 14 1.8912 - 1.8451 1.00 2624 149 0.1761 0.2083 REMARK 3 15 1.8451 - 1.8031 1.00 2699 123 0.1806 0.2271 REMARK 3 16 1.8031 - 1.7648 1.00 2605 138 0.1820 0.2060 REMARK 3 17 1.7648 - 1.7295 1.00 2636 159 0.1809 0.2304 REMARK 3 18 1.7295 - 1.6969 1.00 2637 149 0.1924 0.2129 REMARK 3 19 1.6969 - 1.6666 1.00 2671 153 0.2004 0.2335 REMARK 3 20 1.6666 - 1.6383 1.00 2665 126 0.1994 0.2429 REMARK 3 21 1.6383 - 1.6119 1.00 2625 135 0.2156 0.2463 REMARK 3 22 1.6119 - 1.5871 1.00 2654 139 0.2283 0.2418 REMARK 3 23 1.5871 - 1.5638 0.99 2637 137 0.2386 0.2507 REMARK 3 24 1.5638 - 1.5417 0.97 2587 118 0.2466 0.2878 REMARK 3 25 1.5417 - 1.5209 0.90 2363 130 0.2604 0.2995 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 : 0.40 REMARK 3 B_SOL : 59.59 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.930 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.15 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.90 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.76880 REMARK 3 B22 (A**2) : -0.76880 REMARK 3 B33 (A**2) : 1.53760 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 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 : 0.011 4116 REMARK 3 ANGLE : 1.137 5640 REMARK 3 CHIRALITY : 0.069 627 REMARK 3 PLANARITY : 0.005 648 REMARK 3 DIHEDRAL : 18.006 1615 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 6 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ( CHAIN A AND ( RESID -2:15 OR RESID 88:239 ) ) REMARK 3 ORIGIN FOR THE GROUP (A): 67.6864 -5.2166 -1.7836 REMARK 3 T TENSOR REMARK 3 T11: 0.0633 T22: 0.0385 REMARK 3 T33: 0.0800 T12: 0.0098 REMARK 3 T13: -0.0011 T23: 0.0160 REMARK 3 L TENSOR REMARK 3 L11: 0.7593 L22: 1.1411 REMARK 3 L33: 0.6365 L12: -0.5391 REMARK 3 L13: -0.1032 L23: -0.1680 REMARK 3 S TENSOR REMARK 3 S11: 0.0230 S12: 0.0238 S13: 0.0215 REMARK 3 S21: -0.0660 S22: -0.0640 S23: -0.2067 REMARK 3 S31: 0.0446 S32: 0.0490 S33: 0.0446 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: ( CHAIN A AND ( RESID 16:87 OR RESID 601:603 ) ) REMARK 3 ORIGIN FOR THE GROUP (A): 48.6972 13.3391 11.1795 REMARK 3 T TENSOR REMARK 3 T11: 0.1315 T22: 0.1023 REMARK 3 T33: 0.0849 T12: 0.0108 REMARK 3 T13: 0.0026 T23: -0.0001 REMARK 3 L TENSOR REMARK 3 L11: 0.4433 L22: 0.4637 REMARK 3 L33: 0.4632 L12: 0.0248 REMARK 3 L13: -0.0324 L23: 0.0269 REMARK 3 S TENSOR REMARK 3 S11: 0.0092 S12: -0.1155 S13: 0.0126 REMARK 3 S21: 0.0369 S22: -0.0677 S23: 0.0249 REMARK 3 S31: -0.0993 S32: -0.0026 S33: 0.0449 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: ( CHAIN A AND RESID 240:306 ) REMARK 3 ORIGIN FOR THE GROUP (A): 51.6199 -22.1959 6.1206 REMARK 3 T TENSOR REMARK 3 T11: 0.1024 T22: 0.0937 REMARK 3 T33: 0.1048 T12: -0.0005 REMARK 3 T13: -0.0195 T23: 0.0004 REMARK 3 L TENSOR REMARK 3 L11: 0.4242 L22: 0.6274 REMARK 3 L33: 0.5892 L12: 0.3487 REMARK 3 L13: 0.1954 L23: -0.0897 REMARK 3 S TENSOR REMARK 3 S11: -0.0628 S12: -0.0506 S13: 0.0429 REMARK 3 S21: -0.0555 S22: 0.0065 S23: 0.1024 REMARK 3 S31: 0.0833 S32: -0.1005 S33: 0.0351 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: ( CHAIN A AND RESID 307:432 ) REMARK 3 ORIGIN FOR THE GROUP (A): 30.7093 5.7268 -7.7638 REMARK 3 T TENSOR REMARK 3 T11: 0.1459 T22: 0.2508 REMARK 3 T33: 0.1541 T12: 0.0092 REMARK 3 T13: 0.0103 T23: -0.0686 REMARK 3 L TENSOR REMARK 3 L11: 0.3540 L22: 1.4630 REMARK 3 L33: 1.1044 L12: -0.2880 REMARK 3 L13: 0.3119 L23: 0.7710 REMARK 3 S TENSOR REMARK 3 S11: 0.1406 S12: 0.1459 S13: 0.0632 REMARK 3 S21: -0.1392 S22: -0.3480 S23: 0.2276 REMARK 3 S31: 0.0423 S32: -0.4121 S33: 0.2171 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: ( CHAIN T AND RESID 1:12 ) REMARK 3 ORIGIN FOR THE GROUP (A): 38.1116 -3.1104 -0.4675 REMARK 3 T TENSOR REMARK 3 T11: 0.2494 T22: 0.2328 REMARK 3 T33: 0.2333 T12: -0.0453 REMARK 3 T13: -0.0487 T23: 0.0235 REMARK 3 L TENSOR REMARK 3 L11: 0.4412 L22: 3.5509 REMARK 3 L33: 0.7098 L12: 1.2094 REMARK 3 L13: 0.5134 L23: 1.5710 REMARK 3 S TENSOR REMARK 3 S11: 0.2837 S12: -0.1903 S13: -0.1009 REMARK 3 S21: -0.0311 S22: -0.2986 S23: -0.3662 REMARK 3 S31: 0.0119 S32: -0.4609 S33: -0.0319 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: ( CHAIN P AND ( RESID 1:9 OR RESID 504:506 ) ) REMARK 3 ORIGIN FOR THE GROUP (A): 40.6605 -4.5312 0.1341 REMARK 3 T TENSOR REMARK 3 T11: 0.1700 T22: 0.1402 REMARK 3 T33: 0.1727 T12: 0.0243 REMARK 3 T13: -0.0252 T23: -0.0139 REMARK 3 L TENSOR REMARK 3 L11: 1.9436 L22: 2.0231 REMARK 3 L33: 0.9268 L12: 1.9814 REMARK 3 L13: 1.2181 L23: 1.2713 REMARK 3 S TENSOR REMARK 3 S11: -0.0040 S12: -0.1747 S13: -0.2505 REMARK 3 S21: -0.3370 S22: -0.0327 S23: -0.2773 REMARK 3 S31: -0.2494 S32: -0.1755 S33: 0.0107 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 4ECV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 20-APR-12. REMARK 100 THE DEPOSITION ID IS D_1000071457. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-AUG-11 REMARK 200 TEMPERATURE (KELVIN) : 95 REMARK 200 PH : 6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 69457 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.520 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 (%) : 99.3 REMARK 200 DATA REDUNDANCY : 2.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07300 REMARK 200 FOR THE DATA SET : 11.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.52 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.55 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.8 REMARK 200 DATA REDUNDANCY IN SHELL : 2.30 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.52500 REMARK 200 FOR SHELL : 1.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.74 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M MES, 6-17%(W/V) PEG 2K-MME, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K, PH 6 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 27.47700 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 54.95400 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 41.21550 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 68.69250 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 13.73850 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: 6520 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21990 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -76.0 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: 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 T 7 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DC T 9 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 DG P 2 O4' - C1' - N9 ANGL. DEV. = 1.8 DEGREES REMARK 500 DA P 7 O4' - C4' - C3' ANGL. DEV. = -3.0 DEGREES REMARK 500 DA P 7 O4' - C1' - N9 ANGL. DEV. = 2.2 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 64.24 24.27 REMARK 500 TYR A 39 178.68 67.29 REMARK 500 LYS A 40 -34.74 -152.57 REMARK 500 SER A 62 -13.18 84.43 REMARK 500 ASP A 181 32.55 73.63 REMARK 500 LEU A 183 -165.97 -110.34 REMARK 500 SER A 217 -159.33 -154.38 REMARK 500 SER A 257 -10.97 96.88 REMARK 500 SER A 409 131.18 -39.93 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 CA A 502 AND MG A 503 ARE IN ALTERNATE CONFORMATIONS OF EACH OTHER. 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 501 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 13 OD2 REMARK 620 2 ASP A 115 OD2 93.5 REMARK 620 3 GLU A 116 OE2 103.8 100.6 REMARK 620 4 HOH A 604 O 85.5 167.7 91.5 REMARK 620 5 DT P 8 O3' 177.1 84.4 78.6 96.1 REMARK 620 6 DT P 8 O3' 166.6 84.3 89.5 93.8 11.1 REMARK 620 7 DA P 9 OP1 99.6 82.7 156.0 85.4 78.1 67.0 REMARK 620 8 DTP P 504 O2A 90.7 87.0 163.0 80.7 87.2 76.1 9.8 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 502 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 13 OD1 REMARK 620 2 MET A 14 O 86.6 REMARK 620 3 ASP A 115 OD1 99.1 83.2 REMARK 620 4 DTP P 504 O2A 95.4 175.1 92.1 REMARK 620 5 DTP P 504 O1B 170.0 92.3 90.6 86.5 REMARK 620 6 DTP P 504 O3G 89.8 94.7 170.7 89.8 80.3 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 MET A 14 O 75.0 REMARK 620 3 ASP A 115 OD1 110.0 82.6 REMARK 620 4 DA P 9 OP1 109.6 165.9 83.3 REMARK 620 5 DPO P 505 O2 156.4 93.4 88.2 86.7 REMARK 620 6 DPO P 505 O7 79.4 97.4 170.0 96.6 81.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG P 506 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 602 O REMARK 620 2 HOH A 653 O 89.4 REMARK 620 3 HOH A 841 O 89.0 92.2 REMARK 620 4 HOH A 889 O 167.0 87.5 78.5 REMARK 620 5 DA P 9 OP2 92.8 174.5 82.8 89.2 REMARK 620 6 DPO P 505 O1 98.1 96.6 168.7 94.8 88.0 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 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA 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 DTP P 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DPO P 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 507 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 508 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG P 506 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4ECQ RELATED DB: PDB REMARK 900 RELATED ID: 4ECR RELATED DB: PDB REMARK 900 RELATED ID: 4ECS RELATED DB: PDB REMARK 900 RELATED ID: 4ECT RELATED DB: PDB REMARK 900 RELATED ID: 4ECU RELATED DB: PDB REMARK 900 RELATED ID: 4ECW RELATED DB: PDB REMARK 900 RELATED ID: 4ECX RELATED DB: PDB REMARK 900 RELATED ID: 4ECY RELATED DB: PDB REMARK 900 RELATED ID: 4ECZ RELATED DB: PDB REMARK 900 RELATED ID: 4ED0 RELATED DB: PDB REMARK 900 RELATED ID: 4ED1 RELATED DB: PDB REMARK 900 RELATED ID: 4ED2 RELATED DB: PDB REMARK 900 RELATED ID: 4ED3 RELATED DB: PDB REMARK 900 RELATED ID: 4ED6 RELATED DB: PDB REMARK 900 RELATED ID: 4ED7 RELATED DB: PDB REMARK 900 RELATED ID: 4ED8 RELATED DB: PDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 ARG A 61 HAS THE FOLLOWING ALTERNATE CONFIGURATION. REMARK 999 ALTERNATE A HAS ARG 61 (OCCUPANCY 0.40) + HOH A 601, REMARK 999 ALTERNATE B HAS ARG 61 (OCCUPANCY 0.60) + HOH A 602 + HOH A 603. REMARK 999 CHAIN P HAS THE FOLLOWING ALTERNATE CONFIGURATION. REMARK 999 ALTERNATE A HAS DT 8 + DTP 504, REMARK 999 ALTERNATE B HAS DT 8 + DA 9 + DPO 505 + MG 506. DBREF 4ECV A 1 432 UNP Q9Y253 POLH_HUMAN 1 432 DBREF 4ECV T 1 12 PDB 4ECV 4ECV 1 12 DBREF 4ECV P 1 9 PDB 4ECV 4ECV 1 9 SEQADV 4ECV GLY A -2 UNP Q9Y253 EXPRESSION TAG SEQADV 4ECV PRO A -1 UNP Q9Y253 EXPRESSION TAG SEQADV 4ECV 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 DT DA DT DG DA DC DG DC DT SEQRES 1 P 9 DA DG DC DG DT DC DA DT DA HET MG A 501 1 HET CA A 502 1 HET MG A 503 1 HET GOL A 506 6 HET GOL A 507 6 HET GOL A 508 6 HET DTP P 504 30 HET DPO P 505 9 HET MG P 506 1 HETNAM MG MAGNESIUM ION HETNAM CA CALCIUM ION HETNAM GOL GLYCEROL HETNAM DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE HETNAM DPO DIPHOSPHATE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 4 MG 3(MG 2+) FORMUL 5 CA CA 2+ FORMUL 7 GOL 3(C3 H8 O3) FORMUL 10 DTP C10 H16 N5 O12 P3 FORMUL 11 DPO O7 P2 4- FORMUL 13 HOH *463(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 GLN A 133 1 13 HELIX 7 7 SER A 138 LEU A 142 5 5 HELIX 8 8 GLN A 162 LEU A 178 1 17 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 239 GLY A 241 5 3 HELIX 12 12 SER A 242 GLN A 249 1 8 HELIX 13 13 MET A 250 ILE A 255 5 6 HELIX 14 14 GLY A 260 GLY A 271 1 12 HELIX 15 15 TYR A 274 PHE A 281 5 8 HELIX 16 16 THR A 282 GLY A 291 1 10 HELIX 17 17 GLY A 291 CYS A 302 1 12 HELIX 18 18 PRO A 326 ALA A 330 5 5 HELIX 19 19 ARG A 334 ASP A 360 1 27 HELIX 20 20 ASP A 391 LYS A 404 1 14 HELIX 21 21 ASN A 405 ASN A 407 5 3 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 ALA A 10 O VAL A 119 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 OD2BASP A 13 MG MG A 501 1555 1555 2.03 LINK OD1AASP A 13 CA A CA A 502 1555 1555 2.27 LINK OD1BASP A 13 MG B MG A 503 1555 1555 2.25 LINK O MET A 14 CA A CA A 502 1555 1555 2.25 LINK O MET A 14 MG B MG A 503 1555 1555 2.26 LINK OD2 ASP A 115 MG MG A 501 1555 1555 2.35 LINK OD1 ASP A 115 CA A CA A 502 1555 1555 2.25 LINK OD1 ASP A 115 MG B MG A 503 1555 1555 2.26 LINK OE2 GLU A 116 MG MG A 501 1555 1555 2.12 LINK MG MG A 501 O HOH A 604 1555 1555 2.18 LINK MG MG A 501 O3'A DT P 8 1555 1555 2.26 LINK MG MG A 501 O3'B DT P 8 1555 1555 2.46 LINK MG MG A 501 OP1B DA P 9 1555 1555 2.04 LINK MG MG A 501 O2AADTP P 504 1555 1555 2.34 LINK CA A CA A 502 O2AADTP P 504 1555 1555 2.09 LINK CA A CA A 502 O1BADTP P 504 1555 1555 2.09 LINK CA A CA A 502 O3GADTP P 504 1555 1555 2.21 LINK MG B MG A 503 OP1B DA P 9 1555 1555 2.40 LINK MG B MG A 503 O2 BDPO P 505 1555 1555 2.20 LINK MG B MG A 503 O7 BDPO P 505 1555 1555 2.21 LINK O BHOH A 602 MG B MG P 506 1555 1555 2.09 LINK O HOH A 653 MG B MG P 506 1555 1555 2.57 LINK O HOH A 841 MG B MG P 506 1555 1555 2.19 LINK O HOH A 889 MG B MG P 506 1555 1555 2.55 LINK OP2B DA P 9 MG B MG P 506 1555 1555 2.23 LINK O1 BDPO P 505 MG B MG P 506 1555 1555 2.05 CISPEP 1 LEU A 150 PRO A 151 0 1.92 CISPEP 2 LYS A 231 PRO A 232 0 -2.15 CISPEP 3 SER A 416 PRO A 417 0 -4.74 SITE 1 AC1 9 ASP A 13 ASP A 115 GLU A 116 CA A 502 SITE 2 AC1 9 MG A 503 HOH A 604 DT P 8 DA P 9 SITE 3 AC1 9 DTP P 504 SITE 1 AC2 7 ASP A 13 MET A 14 ASP A 115 MG A 501 SITE 2 AC2 7 DA P 9 DTP P 504 DPO P 505 SITE 1 AC3 7 ASP A 13 MET A 14 ASP A 115 MG A 501 SITE 2 AC3 7 DA P 9 DTP P 504 DPO P 505 SITE 1 AC4 30 ASP A 13 MET A 14 ASP A 15 CYS A 16 SITE 2 AC4 30 PHE A 17 PHE A 18 ILE A 48 ALA A 49 SITE 3 AC4 30 TYR A 52 ARG A 55 ARG A 61 ASP A 115 SITE 4 AC4 30 LYS A 231 MG A 501 CA A 502 MG A 503 SITE 5 AC4 30 HOH A 602 HOH A 603 HOH A 604 HOH A 611 SITE 6 AC4 30 HOH A 653 HOH A 673 HOH A 841 HOH A 867 SITE 7 AC4 30 HOH A 889 HOH A 939 DT P 8 DT T 3 SITE 8 AC4 30 DT T 4 DA T 5 SITE 1 AC5 19 ASP A 13 MET A 14 ASP A 15 CYS A 16 SITE 2 AC5 19 PHE A 17 TYR A 52 ARG A 55 ARG A 61 SITE 3 AC5 19 ASP A 115 LYS A 231 CA A 502 MG A 503 SITE 4 AC5 19 HOH A 603 HOH A 611 HOH A 653 HOH A 889 SITE 5 AC5 19 HOH A 939 DA P 9 MG P 506 SITE 1 AC6 9 ARG A 24 PRO A 244 SER A 248 GLY A 276 SITE 2 AC6 9 GLU A 277 HOH A 609 HOH A 627 HOH A 688 SITE 3 AC6 9 HOH A 703 SITE 1 AC7 9 GLU A 94 ALA A 95 GLU A 98 ARG A 303 SITE 2 AC7 9 HOH A 642 HOH A 647 HOH A 807 HOH A 824 SITE 3 AC7 9 HOH A 972 SITE 1 AC8 10 ASN A 26 PRO A 27 HIS A 28 GLY A 271 SITE 2 AC8 10 GLU A 273 TYR A 274 GLU A 277 HOH A 771 SITE 3 AC8 10 HOH A 803 HOH A 865 SITE 1 AC9 7 ARG A 61 HOH A 602 HOH A 653 HOH A 841 SITE 2 AC9 7 HOH A 889 DA P 9 DPO P 505 CRYST1 98.786 98.786 82.431 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 0.010123 0.005844 0.000000 0.00000 SCALE2 0.000000 0.011689 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012131 0.00000