PDB Short entry for 4ED8 HEADER TRANSFERASE/DNA 27-MAR-12 4ED8 TITLE HUMAN DNA POLYMERASE ETA - DNA TERNARY COMPLEX: REACTION IN THE TG TITLE 2 CRYSTAL AT PH 7.0, NORMAL TRANSLOCATION 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*G)-3'); COMPND 10 CHAIN: T; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: DNA (5'-D(*TP*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 4ED8 1 REMARK SEQADV LINK REVDAT 2 25-JUL-12 4ED8 1 JRNL REVDAT 1 11-JUL-12 4ED8 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) : 28.52 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.0 REMARK 3 NUMBER OF REFLECTIONS : 67241 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 : 0.200 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.050 REMARK 3 FREE R VALUE TEST SET COUNT : 3397 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 28.5221 - 4.3821 0.97 2777 141 0.1643 0.1795 REMARK 3 2 4.3821 - 3.4802 1.00 2753 181 0.1415 0.1732 REMARK 3 3 3.4802 - 3.0408 1.00 2776 144 0.1585 0.1865 REMARK 3 4 3.0408 - 2.7631 1.00 2790 140 0.1777 0.2150 REMARK 3 5 2.7631 - 2.5652 0.99 2748 145 0.1707 0.1947 REMARK 3 6 2.5652 - 2.4140 0.99 2765 137 0.1724 0.1920 REMARK 3 7 2.4140 - 2.2932 0.99 2738 140 0.1602 0.1847 REMARK 3 8 2.2932 - 2.1934 0.99 2738 167 0.1552 0.2026 REMARK 3 9 2.1934 - 2.1090 0.99 2717 147 0.1590 0.1952 REMARK 3 10 2.1090 - 2.0362 0.98 2754 150 0.1621 0.1947 REMARK 3 11 2.0362 - 1.9726 0.99 2722 152 0.1617 0.2123 REMARK 3 12 1.9726 - 1.9162 0.99 2731 140 0.1656 0.2143 REMARK 3 13 1.9162 - 1.8658 0.98 2709 132 0.1723 0.2096 REMARK 3 14 1.8658 - 1.8202 0.98 2770 139 0.1806 0.2017 REMARK 3 15 1.8202 - 1.7789 0.98 2680 157 0.1813 0.2293 REMARK 3 16 1.7789 - 1.7410 0.98 2716 137 0.1890 0.2398 REMARK 3 17 1.7410 - 1.7062 0.98 2706 141 0.1883 0.2060 REMARK 3 18 1.7062 - 1.6740 0.98 2640 160 0.1944 0.2375 REMARK 3 19 1.6740 - 1.6441 0.98 2694 156 0.2014 0.2194 REMARK 3 20 1.6441 - 1.6162 0.98 2697 154 0.2057 0.2350 REMARK 3 21 1.6162 - 1.5902 0.96 2685 117 0.2254 0.2497 REMARK 3 22 1.5902 - 1.5657 0.93 2572 118 0.2291 0.2552 REMARK 3 23 1.5657 - 1.5427 0.80 2227 118 0.2390 0.2831 REMARK 3 24 1.5427 - 1.5210 0.63 1739 84 0.2544 0.2674 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 : 0.34 REMARK 3 B_SOL : 42.00 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.180 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.41 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.59060 REMARK 3 B22 (A**2) : -1.59060 REMARK 3 B33 (A**2) : 3.18110 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 : 0.023 3996 REMARK 3 ANGLE : 1.133 5476 REMARK 3 CHIRALITY : 0.066 613 REMARK 3 PLANARITY : 0.005 629 REMARK 3 DIHEDRAL : 17.904 1559 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): 67.1441 -4.7428 -1.6629 REMARK 3 T TENSOR REMARK 3 T11: 0.0807 T22: 0.0571 REMARK 3 T33: 0.0864 T12: 0.0052 REMARK 3 T13: 0.0003 T23: 0.0197 REMARK 3 L TENSOR REMARK 3 L11: 0.9302 L22: 1.5677 REMARK 3 L33: 0.7600 L12: -0.5991 REMARK 3 L13: -0.0271 L23: -0.2931 REMARK 3 S TENSOR REMARK 3 S11: 0.0260 S12: 0.0413 S13: 0.0155 REMARK 3 S21: -0.0806 S22: -0.0893 S23: -0.2398 REMARK 3 S31: 0.0420 S32: 0.0585 S33: 0.0698 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: ( CHAIN A AND RESID 16:87 ) REMARK 3 ORIGIN FOR THE GROUP (A): 48.7041 13.4468 11.4125 REMARK 3 T TENSOR REMARK 3 T11: 0.1164 T22: 0.0807 REMARK 3 T33: 0.0620 T12: 0.0087 REMARK 3 T13: 0.0087 T23: -0.0006 REMARK 3 L TENSOR REMARK 3 L11: 0.5874 L22: 0.6168 REMARK 3 L33: 0.6304 L12: 0.0253 REMARK 3 L13: 0.1548 L23: -0.1665 REMARK 3 S TENSOR REMARK 3 S11: 0.0230 S12: -0.1051 S13: 0.0274 REMARK 3 S21: 0.0644 S22: -0.0696 S23: 0.0533 REMARK 3 S31: -0.1343 S32: -0.0108 S33: 0.0350 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: ( CHAIN A AND RESID 240:306 ) REMARK 3 ORIGIN FOR THE GROUP (A): 51.5573 -22.0455 6.3147 REMARK 3 T TENSOR REMARK 3 T11: 0.1185 T22: 0.1094 REMARK 3 T33: 0.1045 T12: 0.0071 REMARK 3 T13: -0.0168 T23: 0.0049 REMARK 3 L TENSOR REMARK 3 L11: 0.6124 L22: 0.6645 REMARK 3 L33: 0.6956 L12: 0.3305 REMARK 3 L13: -0.0034 L23: -0.1600 REMARK 3 S TENSOR REMARK 3 S11: -0.0781 S12: -0.0597 S13: 0.0368 REMARK 3 S21: -0.0276 S22: 0.0291 S23: 0.0797 REMARK 3 S31: 0.0939 S32: -0.1263 S33: 0.0281 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: ( CHAIN A AND RESID 307:432 ) REMARK 3 ORIGIN FOR THE GROUP (A): 30.5922 5.7223 -7.5675 REMARK 3 T TENSOR REMARK 3 T11: 0.1115 T22: 0.2456 REMARK 3 T33: 0.2207 T12: -0.0179 REMARK 3 T13: -0.0015 T23: -0.0630 REMARK 3 L TENSOR REMARK 3 L11: 0.1939 L22: 2.2139 REMARK 3 L33: 1.7752 L12: 0.1263 REMARK 3 L13: 0.4191 L23: 0.9425 REMARK 3 S TENSOR REMARK 3 S11: 0.0839 S12: -0.0130 S13: 0.1557 REMARK 3 S21: -0.0746 S22: -0.3226 S23: 0.5256 REMARK 3 S31: 0.0581 S32: -0.5674 S33: 0.2362 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: ( CHAIN T AND RESID 2:12 ) REMARK 3 ORIGIN FOR THE GROUP (A): 37.8078 -5.9506 -1.6874 REMARK 3 T TENSOR REMARK 3 T11: 0.2535 T22: 0.1889 REMARK 3 T33: 0.1928 T12: -0.0004 REMARK 3 T13: -0.0316 T23: 0.0064 REMARK 3 L TENSOR REMARK 3 L11: 0.6145 L22: 3.3597 REMARK 3 L33: 0.2608 L12: 1.0857 REMARK 3 L13: 0.1220 L23: 0.9650 REMARK 3 S TENSOR REMARK 3 S11: 0.1818 S12: -0.0618 S13: -0.1480 REMARK 3 S21: -0.2722 S22: -0.2216 S23: 0.0852 REMARK 3 S31: 0.0036 S32: -0.3246 S33: -0.0066 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: ( CHAIN P AND RESID 1:9 ) REMARK 3 ORIGIN FOR THE GROUP (A): 36.5835 -8.2310 -3.3064 REMARK 3 T TENSOR REMARK 3 T11: 0.3100 T22: 0.1757 REMARK 3 T33: 0.1758 T12: 0.0434 REMARK 3 T13: -0.0328 T23: -0.0224 REMARK 3 L TENSOR REMARK 3 L11: 3.0800 L22: 3.9728 REMARK 3 L33: 1.5121 L12: 1.2940 REMARK 3 L13: 2.0749 L23: 0.9937 REMARK 3 S TENSOR REMARK 3 S11: -0.1762 S12: -0.0856 S13: -0.0104 REMARK 3 S21: -0.9156 S22: -0.0135 S23: -0.1686 REMARK 3 S31: -0.4671 S32: -0.1474 S33: 0.1487 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 4ED8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 26-APR-12. REMARK 100 THE DEPOSITION ID IS D_1000071470. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-AUG-11 REMARK 200 TEMPERATURE (KELVIN) : 95 REMARK 200 PH : 6.0 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 : 67307 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 (%) : 96.4 REMARK 200 DATA REDUNDANCY : 3.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06100 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 16.7000 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 (%) : 71.8 REMARK 200 DATA REDUNDANCY IN SHELL : 2.80 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.63100 REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.600 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 (%): 41.72 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, TEMPERATURE 293K, PH 6.0 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: 5430 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22640 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -59.0 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 465 DC T 1 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 10 O4' - C1' - N9 ANGL. DEV. = -5.4 DEGREES REMARK 500 DT P 8 O4' - C4' - C3' ANGL. DEV. = -3.5 DEGREES REMARK 500 DT P 8 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 DT P 8 O4' - C1' - N1 ANGL. DEV. = 3.7 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 66.49 24.43 REMARK 500 TYR A 39 -176.50 68.97 REMARK 500 LYS A 40 -27.18 -155.07 REMARK 500 SER A 62 -14.22 83.74 REMARK 500 SER A 217 -158.43 -157.51 REMARK 500 SER A 257 -11.58 97.30 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 CA A 503 AND MG A 504 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 502 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 13 OD2 REMARK 620 2 ASP A 115 OD2 97.8 REMARK 620 3 GLU A 116 OE2 102.8 102.0 REMARK 620 4 HOH A 601 O 79.7 162.7 95.2 REMARK 620 5 DA P 9 O3' 173.4 77.3 82.6 103.6 REMARK 620 6 DTP P 501 O2A 96.0 87.4 157.5 75.9 79.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 503 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 13 OD1 REMARK 620 2 ASP A 13 OD2 45.8 REMARK 620 3 MET A 14 O 75.9 109.0 REMARK 620 4 ASP A 115 OD1 115.5 88.2 83.8 REMARK 620 5 DTP P 501 O3G 78.0 103.7 98.3 166.3 REMARK 620 6 DTP P 501 O1B 152.5 158.6 91.0 86.3 80.2 REMARK 620 7 DTP P 501 O2A 111.5 76.1 172.1 90.4 86.1 83.3 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 504 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 13 OD1 REMARK 620 2 MET A 14 O 83.9 REMARK 620 3 ASP A 115 OD1 92.2 82.9 REMARK 620 4 DTP P 501 O3G 102.9 98.0 164.9 REMARK 620 5 DTP P 501 O1B 173.3 89.7 85.1 79.8 REMARK 620 6 DTP P 501 O2A 103.1 170.5 90.4 86.8 83.0 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 DTP P 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 CA A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 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 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: 4ECV 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 DBREF 4ED8 A 1 432 UNP Q9Y253 POLH_HUMAN 1 432 DBREF 4ED8 T 1 12 PDB 4ED8 4ED8 1 12 DBREF 4ED8 P 1 9 PDB 4ED8 4ED8 1 9 SEQADV 4ED8 GLY A -2 UNP Q9Y253 EXPRESSION TAG SEQADV 4ED8 PRO A -1 UNP Q9Y253 EXPRESSION TAG SEQADV 4ED8 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 DG SEQRES 1 P 9 DT DG DC DG DT DC DA DT DA HET MG A 502 1 HET CA A 503 1 HET MG A 504 1 HET GOL A 505 6 HET GOL A 506 6 HET DTP P 501 30 HETNAM MG MAGNESIUM ION HETNAM CA CALCIUM ION HETNAM GOL GLYCEROL HETNAM DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 4 MG 2(MG 2+) FORMUL 5 CA CA 2+ FORMUL 7 GOL 2(C3 H8 O3) FORMUL 9 DTP C10 H16 N5 O12 P3 FORMUL 10 HOH *479(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 SER A 104 1 16 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 OD2AASP A 13 MG MG A 502 1555 1555 2.21 LINK OD1AASP A 13 CA A CA A 503 1555 1555 2.39 LINK OD2AASP A 13 CA A CA A 503 1555 1555 3.02 LINK OD1BASP A 13 MG B MG A 504 1555 1555 2.12 LINK O MET A 14 CA A CA A 503 1555 1555 2.29 LINK O MET A 14 MG B MG A 504 1555 1555 2.31 LINK OD2 ASP A 115 MG MG A 502 1555 1555 2.43 LINK OD1 ASP A 115 CA A CA A 503 1555 1555 2.24 LINK OD1 ASP A 115 MG B MG A 504 1555 1555 2.26 LINK OE2 GLU A 116 MG MG A 502 1555 1555 2.11 LINK MG MG A 502 O HOH A 601 1555 1555 2.17 LINK MG MG A 502 O3' DA P 9 1555 1555 2.32 LINK MG MG A 502 O2A DTP P 501 1555 1555 2.31 LINK CA A CA A 503 O3G DTP P 501 1555 1555 2.27 LINK CA A CA A 503 O1B DTP P 501 1555 1555 2.28 LINK CA A CA A 503 O2A DTP P 501 1555 1555 2.36 LINK MG B MG A 504 O3G DTP P 501 1555 1555 2.26 LINK MG B MG A 504 O1B DTP P 501 1555 1555 2.31 LINK MG B MG A 504 O2A DTP P 501 1555 1555 2.35 CISPEP 1 LEU A 150 PRO A 151 0 1.15 CISPEP 2 LYS A 231 PRO A 232 0 -1.65 CISPEP 3 SER A 416 PRO A 417 0 -6.79 SITE 1 AC1 26 ASP A 13 MET A 14 ASP A 15 CYS A 16 SITE 2 AC1 26 PHE A 17 PHE A 18 ILE A 48 ALA A 49 SITE 3 AC1 26 TYR A 52 ARG A 55 ARG A 61 ASP A 115 SITE 4 AC1 26 LYS A 231 MG A 502 CA A 503 MG A 504 SITE 5 AC1 26 HOH A 601 HOH A 612 HOH A 641 HOH A 646 SITE 6 AC1 26 HOH A 726 HOH A 905 DA P 9 DA T 2 SITE 7 AC1 26 DT T 3 DT T 4 SITE 1 AC2 8 ASP A 13 ASP A 115 GLU A 116 CA A 503 SITE 2 AC2 8 MG A 504 HOH A 601 DA P 9 DTP P 501 SITE 1 AC3 5 ASP A 13 MET A 14 ASP A 115 MG A 502 SITE 2 AC3 5 DTP P 501 SITE 1 AC4 5 ASP A 13 MET A 14 ASP A 115 MG A 502 SITE 2 AC4 5 DTP P 501 SITE 1 AC5 9 ARG A 24 PRO A 244 SER A 248 GLY A 276 SITE 2 AC5 9 GLU A 277 HOH A 606 HOH A 636 HOH A 705 SITE 3 AC5 9 HOH A 899 SITE 1 AC6 9 ASN A 26 PRO A 27 HIS A 28 GLY A 271 SITE 2 AC6 9 GLU A 273 TYR A 274 GLU A 277 HOH A 742 SITE 3 AC6 9 HOH A 868 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