HEADER NUCLEAR PROTEIN/DNA 31-OCT-18 6MXO TITLE STRUCTURE OF HPOLETA INCORPORATING DCTP OPPOSITE THE 3-PRIME PT(DACH)- TITLE 2 GG 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(*AP*CP*GP*GP*CP*TP*CP*AP*CP*AP*CP*T)-3'); COMPND 9 CHAIN: T; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: DNA (5'-D(*TP*AP*GP*TP*GP*TP*GP*AP*G)-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 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606; SOURCE 13 MOL_ID: 3; SOURCE 14 SYNTHETIC: YES; SOURCE 15 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 16 ORGANISM_COMMON: HUMAN; SOURCE 17 ORGANISM_TAXID: 9606 KEYWDS Y-FAMILY DNA POLYMERASE, PT(DACH)-GG, TRANSFERASE-DNA-INHIBITOR KEYWDS 2 COMPLEX, NUCLEAR PROTEIN, NUCLEAR PROTEIN-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR H.OUZON-SHUBEITA,S.LEE REVDAT 4 11-OCT-23 6MXO 1 LINK REVDAT 3 25-DEC-19 6MXO 1 REMARK REVDAT 2 13-MAR-19 6MXO 1 JRNL REVDAT 1 13-FEB-19 6MXO 0 JRNL AUTH H.OUZON-SHUBEITA,M.BAKER,M.C.KOAG,S.LEE JRNL TITL STRUCTURAL BASIS FOR THE BYPASS OF THE MAJOR OXALIPLATIN-DNA JRNL TITL 2 ADDUCTS BY HUMAN DNA POLYMERASE ETA. JRNL REF BIOCHEM. J. V. 476 747 2019 JRNL REFN ESSN 1470-8728 JRNL PMID 30709915 JRNL DOI 10.1042/BCJ20180848 REMARK 2 REMARK 2 RESOLUTION. 2.04 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0032 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.04 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.86 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 94.9 REMARK 3 NUMBER OF REFLECTIONS : 25945 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.177 REMARK 3 R VALUE (WORKING SET) : 0.175 REMARK 3 FREE R VALUE : 0.230 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1399 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.04 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.09 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1732 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 85.15 REMARK 3 BIN R VALUE (WORKING SET) : 0.2310 REMARK 3 BIN FREE R VALUE SET COUNT : 86 REMARK 3 BIN FREE R VALUE : 0.2980 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3345 REMARK 3 NUCLEIC ACID ATOMS : 373 REMARK 3 HETEROGEN ATOMS : 57 REMARK 3 SOLVENT ATOMS : 110 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.04000 REMARK 3 B22 (A**2) : -0.04000 REMARK 3 B33 (A**2) : 0.13000 REMARK 3 B12 (A**2) : -0.04000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.232 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.190 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.116 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.199 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.947 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.910 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3978 ; 0.018 ; 0.018 REMARK 3 BOND LENGTHS OTHERS (A): 3609 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5465 ; 1.898 ; 1.861 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8317 ; 0.956 ; 3.002 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 426 ; 6.573 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 152 ;40.186 ;24.013 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 623 ;15.326 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 28 ;17.445 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 595 ; 0.206 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4138 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 895 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1710 ; 2.119 ; 2.212 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1709 ; 2.119 ; 2.211 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2134 ; 3.235 ; 3.302 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2135 ; 3.235 ; 3.304 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2268 ; 2.687 ; 2.560 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2269 ; 2.686 ; 2.559 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3332 ; 4.032 ; 3.733 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 4608 ; 5.428 ;18.799 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 4597 ; 5.421 ;18.805 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 6MXO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-OCT-18. REMARK 100 THE DEPOSITION ID IS D_1000237699. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-MAY-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.3 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97648 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28856 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.040 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 (%) : 99.2 REMARK 200 DATA REDUNDANCY : 11.30 REMARK 200 R MERGE (I) : 0.13300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.5400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.04 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.08 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.3 REMARK 200 DATA REDUNDANCY IN SHELL : 9.70 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 4DL2 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.84 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.04 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M MES, 5MM MGCL2, 15-20%PEG2K-MME, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K 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 27.23767 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 54.47533 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 40.85650 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 68.09417 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 13.61883 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: 5090 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21620 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -58.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, T, P REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A -6 REMARK 465 ALA A -5 REMARK 465 HIS A -4 REMARK 465 HIS A -3 REMARK 465 HIS A -2 REMARK 465 HIS A -1 REMARK 465 HIS A 0 REMARK 465 HIS A 1 REMARK 465 THR A 155 REMARK 465 THR A 156 REMARK 465 ALA A 157 REMARK 465 ALA A 433 REMARK 465 PRO A 434 REMARK 465 SER A 435 REMARK 465 DA T 1 REMARK 465 DC T 2 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 GLU A 158 CG CD OE1 OE2 REMARK 470 GLU A 159 CG CD OE1 OE2 REMARK 470 DT P 1 O5' C5' C4' O4' C3' C2' C1' REMARK 470 DT P 1 N1 C2 O2 N3 C4 O4 C5 REMARK 470 DT P 1 C7 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 OP1 DC T 11 O HOH T 201 2.11 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 OE2 GLU A 82 OP2 DT T 12 5444 1.74 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 30 NE - CZ - NH2 ANGL. DEV. = 3.5 DEGREES REMARK 500 ASP A 66 CB - CG - OD1 ANGL. DEV. = 5.6 DEGREES REMARK 500 ARG A 382 NE - CZ - NH1 ANGL. DEV. = 4.7 DEGREES REMARK 500 DC T 7 O5' - P - OP2 ANGL. DEV. = -5.6 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 58.06 26.16 REMARK 500 TYR A 39 62.28 66.30 REMARK 500 GLU A 159 -62.11 -11.72 REMARK 500 THR A 160 2.97 -60.40 REMARK 500 SER A 217 -159.34 -156.88 REMARK 500 SER A 257 -10.88 94.81 REMARK 500 LEU A 381 132.56 179.84 REMARK 500 GLN A 412 -37.20 81.11 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 502 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 13 OD1 REMARK 620 2 MET A 14 O 83.5 REMARK 620 3 ASP A 115 OD2 96.8 85.3 REMARK 620 4 0KX A 501 O1G 84.9 101.5 173.2 REMARK 620 5 0KX A 501 O1B 170.2 89.1 88.9 90.3 REMARK 620 6 0KX A 501 O2A 100.6 169.3 84.4 88.8 87.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 503 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 13 OD2 REMARK 620 2 ASP A 115 OD1 95.5 REMARK 620 3 GLU A 116 OE2 87.5 88.9 REMARK 620 4 0KX A 501 O2A 99.8 89.3 172.6 REMARK 620 5 HOH A 674 O 88.9 168.5 101.9 79.4 REMARK 620 6 DG P 9 O3' 162.2 95.5 78.7 94.3 83.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 9RD T 101 PT REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG T 3 N7 REMARK 620 2 9RD T 101 N1 97.5 REMARK 620 3 9RD T 101 N2 157.4 83.5 REMARK 620 4 DG T 3 N7 18.4 90.5 171.7 REMARK 620 5 DG T 4 N7 100.6 161.0 82.1 104.9 REMARK 620 6 DG T 4 N7 97.3 164.0 85.3 101.7 3.3 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 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 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 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 9RD T 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4DL2 RELATED DB: PDB REMARK 900 RELATED ID: 4DL3 RELATED DB: PDB REMARK 900 RELATED ID: 4DL4 RELATED DB: PDB REMARK 900 RELATED ID: 4DL5 RELATED DB: PDB DBREF 6MXO A 3 435 UNP Q9Y253 POLH_HUMAN 3 435 DBREF 6MXO T 1 12 PDB 6MXO 6MXO 1 12 DBREF 6MXO P 1 9 PDB 6MXO 6MXO 1 9 SEQADV 6MXO MET A -6 UNP Q9Y253 INITIATING METHIONINE SEQADV 6MXO ALA A -5 UNP Q9Y253 EXPRESSION TAG SEQADV 6MXO HIS A -4 UNP Q9Y253 EXPRESSION TAG SEQADV 6MXO HIS A -3 UNP Q9Y253 EXPRESSION TAG SEQADV 6MXO HIS A -2 UNP Q9Y253 EXPRESSION TAG SEQADV 6MXO HIS A -1 UNP Q9Y253 EXPRESSION TAG SEQADV 6MXO HIS A 0 UNP Q9Y253 EXPRESSION TAG SEQADV 6MXO HIS A 1 UNP Q9Y253 EXPRESSION TAG SEQADV 6MXO GLY A 2 UNP Q9Y253 EXPRESSION TAG SEQRES 1 A 442 MET ALA HIS HIS HIS HIS HIS HIS GLY THR GLY GLN ASP SEQRES 2 A 442 ARG VAL VAL ALA LEU VAL ASP MET ASP CYS PHE PHE VAL SEQRES 3 A 442 GLN VAL GLU GLN ARG GLN ASN PRO HIS LEU ARG ASN LYS SEQRES 4 A 442 PRO CYS ALA VAL VAL GLN TYR LYS SER TRP LYS GLY GLY SEQRES 5 A 442 GLY ILE ILE ALA VAL SER TYR GLU ALA ARG ALA PHE GLY SEQRES 6 A 442 VAL THR ARG SER MET TRP ALA ASP ASP ALA LYS LYS LEU SEQRES 7 A 442 CYS PRO ASP LEU LEU LEU ALA GLN VAL ARG GLU SER ARG SEQRES 8 A 442 GLY LYS ALA ASN LEU THR LYS TYR ARG GLU ALA SER VAL SEQRES 9 A 442 GLU VAL MET GLU ILE MET SER ARG PHE ALA VAL ILE GLU SEQRES 10 A 442 ARG ALA SER ILE ASP GLU ALA TYR VAL ASP LEU THR SER SEQRES 11 A 442 ALA VAL GLN GLU ARG LEU GLN LYS LEU GLN GLY GLN PRO SEQRES 12 A 442 ILE SER ALA ASP LEU LEU PRO SER THR TYR ILE GLU GLY SEQRES 13 A 442 LEU PRO GLN GLY PRO THR THR ALA GLU GLU THR VAL GLN SEQRES 14 A 442 LYS GLU GLY MET ARG LYS GLN GLY LEU PHE GLN TRP LEU SEQRES 15 A 442 ASP SER LEU GLN ILE ASP ASN LEU THR SER PRO ASP LEU SEQRES 16 A 442 GLN LEU THR VAL GLY ALA VAL ILE VAL GLU GLU MET ARG SEQRES 17 A 442 ALA ALA ILE GLU ARG GLU THR GLY PHE GLN CYS SER ALA SEQRES 18 A 442 GLY ILE SER HIS ASN LYS VAL LEU ALA LYS LEU ALA CYS SEQRES 19 A 442 GLY LEU ASN LYS PRO ASN ARG GLN THR LEU VAL SER HIS SEQRES 20 A 442 GLY SER VAL PRO GLN LEU PHE SER GLN MET PRO ILE ARG SEQRES 21 A 442 LYS ILE ARG SER LEU GLY GLY LYS LEU GLY ALA SER VAL SEQRES 22 A 442 ILE GLU ILE LEU GLY ILE GLU TYR MET GLY GLU LEU THR SEQRES 23 A 442 GLN PHE THR GLU SER GLN LEU GLN SER HIS PHE GLY GLU SEQRES 24 A 442 LYS ASN GLY SER TRP LEU TYR ALA MET CYS ARG GLY ILE SEQRES 25 A 442 GLU HIS ASP PRO VAL LYS PRO ARG GLN LEU PRO LYS THR SEQRES 26 A 442 ILE GLY CYS SER LYS ASN PHE PRO GLY LYS THR ALA LEU SEQRES 27 A 442 ALA THR ARG GLU GLN VAL GLN TRP TRP LEU LEU GLN LEU SEQRES 28 A 442 ALA GLN GLU LEU GLU GLU ARG LEU THR LYS ASP ARG ASN SEQRES 29 A 442 ASP ASN ASP ARG VAL ALA THR GLN LEU VAL VAL SER ILE SEQRES 30 A 442 ARG VAL GLN GLY ASP LYS ARG LEU SER SER LEU ARG ARG SEQRES 31 A 442 CYS CYS ALA LEU THR ARG TYR ASP ALA HIS LYS MET SER SEQRES 32 A 442 HIS ASP ALA PHE THR VAL ILE LYS ASN CYS ASN THR SER SEQRES 33 A 442 GLY ILE GLN THR GLU TRP SER PRO PRO LEU THR MET LEU SEQRES 34 A 442 PHE LEU CYS ALA THR LYS PHE SER ALA SER ALA PRO SER SEQRES 1 T 12 DA DC DG DG DC DT DC DA DC DA DC DT SEQRES 1 P 9 DT DA DG DT DG DT DG DA DG HET 0KX A 501 28 HET MG A 502 1 HET MG A 503 1 HET GOL A 504 6 HET GOL A 505 6 HET GOL A 506 6 HET 9RD T 101 9 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 HETNAM 9RD (CYCLOHEX-1-ENE-1,2-DIAMINE)PLATINUM(2+) 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 3(C3 H8 O3) FORMUL 10 9RD C6 H12 N2 PT 2+ FORMUL 11 HOH *110(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 ALA A 107 1 19 HELIX 6 AA6 LEU A 121 LEU A 132 1 12 HELIX 7 AA7 SER A 138 LEU A 142 5 5 HELIX 8 AA8 GLU A 158 VAL A 161 5 4 HELIX 9 AA9 GLN A 162 LEU A 178 1 17 HELIX 10 AB1 SER A 185 GLY A 209 1 25 HELIX 11 AB2 ASN A 219 GLY A 228 1 10 HELIX 12 AB3 SER A 239 GLY A 241 5 3 HELIX 13 AB4 SER A 242 GLN A 249 1 8 HELIX 14 AB5 MET A 250 ILE A 255 5 6 HELIX 15 AB6 GLY A 260 GLY A 271 1 12 HELIX 16 AB7 TYR A 274 PHE A 281 5 8 HELIX 17 AB8 THR A 282 GLY A 291 1 10 HELIX 18 AB9 GLY A 291 CYS A 302 1 12 HELIX 19 AC1 PRO A 326 ALA A 330 5 5 HELIX 20 AC2 ARG A 334 ASP A 360 1 27 HELIX 21 AC3 ASP A 391 LYS A 404 1 14 HELIX 22 AC4 ASN A 405 ASN A 407 5 3 SHEET 1 AA1 6 ILE A 109 SER A 113 0 SHEET 2 AA1 6 GLU A 116 ASP A 120 -1 O TYR A 118 N GLU A 110 SHEET 3 AA1 6 VAL A 9 MET A 14 -1 N ALA A 10 O VAL A 119 SHEET 4 AA1 6 CYS A 212 SER A 217 -1 O SER A 217 N VAL A 9 SHEET 5 AA1 6 GLN A 235 LEU A 237 1 O THR A 236 N ILE A 216 SHEET 6 AA1 6 THR A 145 ILE A 147 1 N TYR A 146 O LEU A 237 SHEET 1 AA2 3 GLY A 46 VAL A 50 0 SHEET 2 AA2 3 CYS A 34 GLN A 38 -1 N VAL A 36 O ILE A 48 SHEET 3 AA2 3 LEU A 76 GLN A 79 1 O ALA A 78 N VAL A 37 SHEET 1 AA3 2 GLU A 82 SER A 83 0 SHEET 2 AA3 2 LYS A 86 ALA A 87 -1 O LYS A 86 N SER A 83 SHEET 1 AA4 3 ILE A 319 ASN A 324 0 SHEET 2 AA4 3 GLU A 414 ALA A 431 -1 O ALA A 426 N ILE A 319 SHEET 3 AA4 3 LEU A 331 THR A 333 -1 N LEU A 331 O LEU A 419 SHEET 1 AA5 4 ILE A 319 ASN A 324 0 SHEET 2 AA5 4 GLU A 414 ALA A 431 -1 O ALA A 426 N ILE A 319 SHEET 3 AA5 4 ARG A 361 VAL A 372 -1 N VAL A 367 O CYS A 425 SHEET 4 AA5 4 LEU A 381 ALA A 386 -1 O CYS A 385 N LEU A 366 LINK OD1 ASP A 13 MG MG A 502 1555 1555 1.99 LINK OD2 ASP A 13 MG MG A 503 1555 1555 2.06 LINK O MET A 14 MG MG A 502 1555 1555 2.17 LINK OD2 ASP A 115 MG MG A 502 1555 1555 2.08 LINK OD1 ASP A 115 MG MG A 503 1555 1555 2.16 LINK OE2 GLU A 116 MG MG A 503 1555 1555 2.06 LINK O1G 0KX A 501 MG MG A 502 1555 1555 2.14 LINK O1B 0KX A 501 MG MG A 502 1555 1555 2.08 LINK O2A 0KX A 501 MG MG A 502 1555 1555 2.09 LINK O2A 0KX A 501 MG MG A 503 1555 1555 2.27 LINK MG MG A 503 O HOH A 674 1555 1555 2.27 LINK MG MG A 503 O3' DG P 9 1555 1555 2.20 LINK N7 A DG T 3 PT 9RD T 101 1555 1555 1.91 LINK N7 B DG T 3 PT 9RD T 101 1555 1555 1.99 LINK N7 A DG T 4 PT 9RD T 101 1555 1555 1.93 LINK N7 B DG T 4 PT 9RD T 101 1555 1555 1.90 CISPEP 1 LEU A 150 PRO A 151 0 1.48 CISPEP 2 LYS A 231 PRO A 232 0 2.10 CISPEP 3 SER A 416 PRO A 417 0 -6.84 SITE 1 AC1 21 ASP A 13 MET A 14 ASP A 15 CYS A 16 SITE 2 AC1 21 PHE A 17 PHE A 18 ILE A 48 ALA A 49 SITE 3 AC1 21 TYR A 52 ARG A 55 ARG A 61 ASP A 115 SITE 4 AC1 21 LYS A 231 MG A 502 MG A 503 HOH A 620 SITE 5 AC1 21 HOH A 630 HOH A 666 HOH A 674 DG P 9 SITE 6 AC1 21 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 674 DG P 9 SITE 1 AC4 10 ARG A 24 GLN A 25 PRO A 244 PHE A 247 SITE 2 AC4 10 SER A 248 GLY A 276 GLU A 277 HOH A 608 SITE 3 AC4 10 HOH A 617 HOH A 621 SITE 1 AC5 3 GLN A 20 ARG A 30 GLY A 209 SITE 1 AC6 7 ASN A 26 HIS A 28 GLY A 271 ILE A 272 SITE 2 AC6 7 GLU A 273 TYR A 274 GLU A 277 SITE 1 AC7 5 DA P 8 DG P 9 DG T 3 DG T 4 SITE 2 AC7 5 DC T 5 CRYST1 98.560 98.560 81.713 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 0.010146 0.005858 0.000000 0.00000 SCALE2 0.000000 0.011716 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012238 0.00000