HEADER TRANSFERASE/DNA 05-OCT-18 6MP3 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; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28B; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 14 ORGANISM_TAXID: 32630; SOURCE 15 MOL_ID: 3; SOURCE 16 SYNTHETIC: YES; SOURCE 17 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 18 ORGANISM_TAXID: 32630 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 2 11-OCT-23 6MP3 1 REMARK LINK REVDAT 1 16-OCT-19 6MP3 0 JRNL AUTH M.A.HAWKINS,J.HUNMIN,S.LEE JRNL TITL STRUCTURAL ANALYSIS OF TRANSLESION SYNTHESIS ACROSS JRNL TITL 2 HYPOXANTHINE LESION USING HUMAN DNA POLYMERASE ETA JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.91 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.91 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.72 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 35022 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.170 REMARK 3 R VALUE (WORKING SET) : 0.168 REMARK 3 FREE R VALUE : 0.209 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.770 REMARK 3 FREE R VALUE TEST SET COUNT : 2021 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 42.7274 - 4.5937 1.00 2417 149 0.1811 0.2042 REMARK 3 2 4.5937 - 3.6468 1.00 2366 143 0.1399 0.1851 REMARK 3 3 3.6468 - 3.1860 1.00 2376 150 0.1546 0.1817 REMARK 3 4 3.1860 - 2.8948 1.00 2355 141 0.1699 0.2193 REMARK 3 5 2.8948 - 2.6873 1.00 2385 148 0.1737 0.2033 REMARK 3 6 2.6873 - 2.5289 1.00 2336 147 0.1702 0.2105 REMARK 3 7 2.5289 - 2.4023 1.00 2347 143 0.1713 0.2469 REMARK 3 8 2.4023 - 2.2977 1.00 2369 145 0.1633 0.2006 REMARK 3 9 2.2977 - 2.2093 1.00 2339 144 0.1641 0.1976 REMARK 3 10 2.2093 - 2.1330 1.00 2368 139 0.1736 0.2628 REMARK 3 11 2.1330 - 2.0663 1.00 2366 142 0.1853 0.2508 REMARK 3 12 2.0663 - 2.0073 1.00 2331 144 0.1973 0.2640 REMARK 3 13 2.0073 - 1.9544 1.00 2363 146 0.2092 0.2606 REMARK 3 14 1.9544 - 1.9067 0.98 2283 140 0.2255 0.2822 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.940 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 28.14 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 38.57 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 6MP3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-OCT-18. REMARK 100 THE DEPOSITION ID IS D_1000237192. 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 : 35061 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.910 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 (%) : 100.0 REMARK 200 DATA REDUNDANCY : 10.00 REMARK 200 R MERGE (I) : 0.11900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 4.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.91 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.94 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 9.40 REMARK 200 R MERGE FOR SHELL (I) : 0.99600 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: PHENIX REMARK 200 STARTING MODEL: 4O3N REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.69 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM MES 5.5, PEG 2K MME, 10MM MGSO4, REMARK 280 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 27.08067 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 54.16133 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 40.62100 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 67.70167 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 13.54033 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: 4300 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22170 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -46.0 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 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 284 N CA C O CB 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 H THR A 282 OE1 GLN A 285 1.09 REMARK 500 O HOH A 776 O HOH A 866 1.30 REMARK 500 O HOH A 857 O HOH A 869 1.43 REMARK 500 HH22 ARG A 256 O HOH A 602 1.51 REMARK 500 NA NA A 501 O HOH A 842 1.57 REMARK 500 HE22 GLN A 249 O HOH A 613 1.58 REMARK 500 O HOH A 785 O HOH A 870 1.65 REMARK 500 O LEU A 178 O HOH A 601 1.73 REMARK 500 O HOH A 672 O HOH A 804 1.76 REMARK 500 O HOH A 726 O HOH A 829 1.76 REMARK 500 NH2 ARG A 256 O HOH A 602 1.78 REMARK 500 O HOH P 121 O HOH P 123 1.81 REMARK 500 O HOH A 604 O HOH A 799 1.87 REMARK 500 N THR A 282 OE1 GLN A 285 1.87 REMARK 500 NE2 HIS A 28 O HOH A 603 1.89 REMARK 500 O HOH P 113 O HOH P 121 1.90 REMARK 500 O HOH A 665 O HOH A 683 1.90 REMARK 500 OP2 DA T 8 O HOH T 101 1.91 REMARK 500 OE2 GLU A 306 O HOH A 604 1.98 REMARK 500 O HOH A 621 O HOH A 828 1.98 REMARK 500 OE1 GLU A 101 O HOH A 605 2.01 REMARK 500 OE1 GLN A 79 O HOH A 606 2.02 REMARK 500 SD MET A 100 O HOH A 847 2.04 REMARK 500 O HOH T 116 O HOH P 111 2.04 REMARK 500 SD MET A 100 O HOH A 847 2.05 REMARK 500 O HOH A 788 O HOH A 832 2.05 REMARK 500 OE1 GLN A 179 O HOH A 607 2.10 REMARK 500 O HOH A 642 O HOH A 865 2.13 REMARK 500 O HOH A 601 O HOH A 833 2.13 REMARK 500 O ALA A 264 OE1 GLU A 268 2.14 REMARK 500 O HOH A 630 O HOH A 839 2.15 REMARK 500 OE1 GLN A 179 O HOH A 608 2.18 REMARK 500 OP2 DA T 2 O HOH T 102 2.18 REMARK 500 OP2 DT P 5 O HOH P 101 2.18 REMARK 500 CD GLN A 179 O HOH A 608 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 PRO A 151 HH12 ARG A 389 4565 1.36 REMARK 500 O LEU A 75 HG SER A 288 6555 1.52 REMARK 500 O PRO A 151 NH1 ARG A 389 4565 1.79 REMARK 500 O HOH A 792 O HOH A 829 6555 2.05 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 DT T 6 C5 DT T 6 C7 -0.036 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 DT T 3 O4' - C1' - C2' ANGL. DEV. = 3.1 DEGREES REMARK 500 DG T 7 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 DC T 9 O4' - C1' - N1 ANGL. DEV. = 4.1 DEGREES REMARK 500 DT T 12 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 DG P 2 O4' - C1' - N9 ANGL. DEV. = 1.8 DEGREES REMARK 500 DC P 3 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 DC P 6 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 DA P 7 O4' - C4' - C3' ANGL. DEV. = -3.0 DEGREES REMARK 500 DA P 7 O4' - C1' - N9 ANGL. DEV. = 2.8 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 67.83 24.40 REMARK 500 TYR A 39 -175.82 70.25 REMARK 500 LYS A 40 -32.98 -156.71 REMARK 500 SER A 62 -5.75 73.96 REMARK 500 SER A 113 -177.65 -170.95 REMARK 500 GLN A 133 -142.95 66.14 REMARK 500 SER A 217 -155.57 -157.65 REMARK 500 SER A 257 -10.65 93.61 REMARK 500 GLN A 285 -39.42 -153.77 REMARK 500 PRO A 312 84.33 -69.54 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 SER A 284 GLN A 285 148.35 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 501 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 176 O REMARK 620 2 HOH A 601 O 69.7 REMARK 620 3 HOH A 833 O 70.8 41.0 REMARK 620 4 HOH A 843 O 126.1 94.3 128.3 REMARK 620 5 HOH A 844 O 76.9 137.4 143.7 84.3 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 502 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLN A 179 OE1 REMARK 620 2 SER A 185 OG 108.8 REMARK 620 3 ASP A 187 OD2 76.3 98.5 REMARK 620 4 HOH A 608 O 47.4 116.0 119.8 REMARK 620 5 HOH A 725 O 136.6 77.8 60.3 164.9 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 NA A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 502 DBREF 6MP3 A 1 432 UNP Q9Y253 POLH_HUMAN 1 432 DBREF 6MP3 T 1 12 PDB 6MP3 6MP3 1 12 DBREF 6MP3 P 1 8 PDB 6MP3 6MP3 1 8 SEQADV 6MP3 GLY A -2 UNP Q9Y253 EXPRESSION TAG SEQADV 6MP3 PRO A -1 UNP Q9Y253 EXPRESSION TAG SEQADV 6MP3 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 DI DA DT DG DA DC DG DC DT SEQRES 1 P 8 DA DG DC DG DT DC DA DT HET NA A 501 1 HET NA A 502 1 HETNAM NA SODIUM ION FORMUL 4 NA 2(NA 1+) FORMUL 6 HOH *355(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 SER A 104 1 16 HELIX 6 AA6 LEU A 121 GLN A 133 1 13 HELIX 7 AA7 SER A 138 LEU A 142 5 5 HELIX 8 AA8 GLN A 162 LEU A 178 1 17 HELIX 9 AA9 SER A 185 GLY A 209 1 25 HELIX 10 AB1 ASN A 219 GLY A 228 1 10 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 VAL A 108 ARG A 111 0 SHEET 2 AA1 6 GLU A 116 ASP A 120 -1 O ASP A 120 N VAL A 108 SHEET 3 AA1 6 VAL A 9 MET A 14 -1 N VAL A 12 O ALA A 117 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 THR A 427 -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 THR A 427 -1 O ALA A 426 N ILE A 319 SHEET 3 AA5 4 GLN A 365 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 SHEET 1 AA6 2 ARG A 361 VAL A 362 0 SHEET 2 AA6 2 SER A 430 ALA A 431 -1 O SER A 430 N VAL A 362 LINK O ASP A 176 NA NA A 501 1555 1555 2.96 LINK OE1 GLN A 179 NA NA A 502 1555 1555 2.96 LINK OG SER A 185 NA NA A 502 1555 1555 2.72 LINK OD2 ASP A 187 NA NA A 502 1555 1555 3.10 LINK NA NA A 501 O HOH A 601 1555 1555 2.90 LINK NA NA A 501 O HOH A 833 1555 1555 3.15 LINK NA NA A 501 O HOH A 843 1555 1555 2.88 LINK NA NA A 501 O HOH A 844 1555 1555 2.40 LINK NA NA A 502 O HOH A 608 1555 1555 2.05 LINK NA NA A 502 O HOH A 725 1555 1555 2.38 CISPEP 1 LEU A 150 PRO A 151 0 1.98 CISPEP 2 LYS A 231 PRO A 232 0 -5.01 CISPEP 3 SER A 416 PRO A 417 0 -6.00 SITE 1 AC1 6 ASP A 176 LEU A 178 HOH A 601 HOH A 842 SITE 2 AC1 6 HOH A 843 HOH A 844 SITE 1 AC2 5 GLN A 179 SER A 185 ASP A 187 HOH A 608 SITE 2 AC2 5 HOH A 725 CRYST1 98.650 98.650 81.242 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 0.010137 0.005853 0.000000 0.00000 SCALE2 0.000000 0.011705 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012309 0.00000