HEADER TRANSFERASE/DNA 18-NOV-14 4RU9 TITLE CRYSTAL STRUCTURE OF HUMAN DNA POLYMERASE ETA INSERTING DCMPNPP TITLE 2 OPPOSITE A MEFAPY-DG ADDUCTED DNA TEMPLATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE ETA; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: 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: NUCLEIC ACIDS TEMPLATE: CAT(MF7)ATGACGCT; COMPND 10 CHAIN: T; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: NUCLEIC ACIDS PRIMAR: AGCGTCAT; 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 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 11 ORGANISM_TAXID: 32630; SOURCE 12 OTHER_DETAILS: CHEMICALLY SYNTHESIZED; SOURCE 13 MOL_ID: 3; SOURCE 14 SYNTHETIC: YES; SOURCE 15 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 16 ORGANISM_TAXID: 32630; SOURCE 17 OTHER_DETAILS: CHEMICALLY SYNTHESIZED KEYWDS DNA DAMAGE, DNA-DIRECTED DNA POLYMERASE, CYTIDINE TRIPHOSPHATE, Y- KEYWDS 2 FAMILY POLYMERASE, TRANS-LESION SYNTHESIS (TLS), DNA BINDING, KEYWDS 3 MEFAPY-DG LESION BYPASS, 2, 6-DIAMINO-4-HYDROXY-N(5)-(METHYL)- KEYWDS 4 FORMAMIDOPYRIMIDINE (MEFAPY-DG) LESION, TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR A.PATRA,M.EGLI REVDAT 2 20-SEP-23 4RU9 1 REMARK LINK REVDAT 1 05-AUG-15 4RU9 0 JRNL AUTH A.PATRA,S.BANERJEE,T.L.JOHNSON SALYARD,C.K.MALIK, JRNL AUTH 2 P.P.CHRISTOV,C.J.RIZZO,M.P.STONE,M.EGLI JRNL TITL STRUCTURAL BASIS FOR ERROR-FREE BYPASS OF THE JRNL TITL 2 5-N-METHYLFORMAMIDOPYRIMIDINE-DG LESION BY HUMAN DNA JRNL TITL 3 POLYMERASE ETA AND SULFOLOBUS SOLFATARICUS P2 POLYMERASE IV. JRNL REF J.AM.CHEM.SOC. V. 137 7011 2015 JRNL REFN ISSN 0002-7863 JRNL PMID 25988947 JRNL DOI 10.1021/JACS.5B02701 REMARK 2 REMARK 2 RESOLUTION. 2.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0073 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 12503 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) : 0.162 REMARK 3 R VALUE (WORKING SET) : 0.159 REMARK 3 FREE R VALUE : 0.229 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 688 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) : 2.65 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.72 REMARK 3 REFLECTION IN BIN (WORKING SET) : 934 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.80 REMARK 3 BIN R VALUE (WORKING SET) : 0.2210 REMARK 3 BIN FREE R VALUE SET COUNT : 46 REMARK 3 BIN FREE R VALUE : 0.3410 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3345 REMARK 3 NUCLEIC ACID ATOMS : 391 REMARK 3 HETEROGEN ATOMS : 30 REMARK 3 SOLVENT ATOMS : 138 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 47.75 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.16000 REMARK 3 B22 (A**2) : -0.16000 REMARK 3 B33 (A**2) : 0.52000 REMARK 3 B12 (A**2) : -0.08000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.347 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.255 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 12.338 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.958 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.923 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3880 ; 0.011 ; 0.018 REMARK 3 BOND LENGTHS OTHERS (A): 3566 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5318 ; 1.512 ; 1.883 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8218 ; 1.408 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 429 ; 6.353 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 152 ;37.059 ;24.013 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 632 ;16.922 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 28 ;20.054 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 579 ; 0.086 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4100 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 877 ; 0.002 ; 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): 1713 ; 3.012 ; 4.508 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1712 ; 3.011 ; 4.506 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2140 ; 4.787 ; 6.745 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2141 ; 4.739 ; 6.797 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2167 ; 3.502 ; 5.088 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2168 ; 3.569 ; 5.123 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3178 ; 5.684 ; 7.566 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 16437 ; 9.870 ;44.011 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 16392 ; 9.868 ;44.009 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 : MASK 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 4RU9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-NOV-14. REMARK 100 THE DEPOSITION ID IS D_1000087803. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-AUG-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.07810 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16058 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.480 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 5.500 REMARK 200 R MERGE (I) : 0.14500 REMARK 200 R SYM (I) : 0.14500 REMARK 200 FOR THE DATA SET : 11.7810 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.48 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.52 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.30 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.026 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER (MR) REMARK 200 STARTING MODEL: PDB ENTRY 4O3N REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.37 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.13 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MES PH 5.5, 5MM MAGNESIUM REMARK 280 CHLORIDE, 25% PEG 2000 MME , VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 291.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 27.20800 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 54.41600 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 40.81200 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 68.02000 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 13.60400 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: 4310 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21870 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -41.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, T, P REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 THR A 155 REMARK 465 THR A 156 REMARK 465 ALA A 157 REMARK 465 GLU A 158 REMARK 465 GLU A 159 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 DC T 1 O5' C5' C4' O4' C3' C2' C1' REMARK 470 DC T 1 N1 C2 O2 N3 C4 N4 C5 REMARK 470 DC T 1 C6 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OG1 THR A 3 OE1 GLN A 5 1.95 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 MF7 T 4 C3' - O3' - P ANGL. DEV. = -8.3 DEGREES REMARK 500 DA T 5 O3' - P - OP2 ANGL. DEV. = 15.9 DEGREES REMARK 500 DA T 5 O3' - P - OP1 ANGL. DEV. = -25.0 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 THR A 3 40.14 21.00 REMARK 500 CYS A 16 65.91 25.89 REMARK 500 TYR A 39 86.53 64.47 REMARK 500 SER A 62 45.60 71.03 REMARK 500 SER A 217 -158.55 -157.85 REMARK 500 SER A 257 -2.96 78.71 REMARK 500 ALA A 332 26.84 -142.06 REMARK 500 ASP A 375 144.74 -36.94 REMARK 500 LEU A 378 -80.27 -8.54 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 502 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 13 OD2 REMARK 620 2 MET A 14 O 76.0 REMARK 620 3 ASP A 115 OD2 91.8 84.5 REMARK 620 4 0KX A 501 O1B 161.8 87.8 95.1 REMARK 620 5 0KX A 501 O1A 106.2 175.8 98.9 89.4 REMARK 620 6 0KX A 501 O3G 87.6 92.4 176.9 84.7 84.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 503 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 13 OD1 REMARK 620 2 ASP A 115 OD1 87.3 REMARK 620 3 GLU A 116 OE2 75.5 84.3 REMARK 620 4 0KX A 501 O1A 98.8 105.1 169.0 REMARK 620 5 HOH A 617 O 78.7 162.6 82.3 87.3 REMARK 620 6 DT P 8 O3' 153.9 83.9 79.2 107.2 104.3 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 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4RUA RELATED DB: PDB DBREF 4RU9 A 1 432 UNP Q9Y253 POLH_HUMAN 1 432 DBREF 4RU9 T 1 12 PDB 4RU9 4RU9 1 12 DBREF 4RU9 P 1 8 PDB 4RU9 4RU9 1 8 SEQRES 1 A 432 MET ALA THR GLY GLN ASP ARG VAL VAL ALA LEU VAL ASP SEQRES 2 A 432 MET ASP CYS PHE PHE VAL GLN VAL GLU GLN ARG GLN ASN SEQRES 3 A 432 PRO HIS LEU ARG ASN LYS PRO CYS ALA VAL VAL GLN TYR SEQRES 4 A 432 LYS SER TRP LYS GLY GLY GLY ILE ILE ALA VAL SER TYR SEQRES 5 A 432 GLU ALA ARG ALA PHE GLY VAL THR ARG SER MET TRP ALA SEQRES 6 A 432 ASP ASP ALA LYS LYS LEU CYS PRO ASP LEU LEU LEU ALA SEQRES 7 A 432 GLN VAL ARG GLU SER ARG GLY LYS ALA ASN LEU THR LYS SEQRES 8 A 432 TYR ARG GLU ALA SER VAL GLU VAL MET GLU ILE MET SER SEQRES 9 A 432 ARG PHE ALA VAL ILE GLU ARG ALA SER ILE ASP GLU ALA SEQRES 10 A 432 TYR VAL ASP LEU THR SER ALA VAL GLN GLU ARG LEU GLN SEQRES 11 A 432 LYS LEU GLN GLY GLN PRO ILE SER ALA ASP LEU LEU PRO SEQRES 12 A 432 SER THR TYR ILE GLU GLY LEU PRO GLN GLY PRO THR THR SEQRES 13 A 432 ALA GLU GLU THR VAL GLN LYS GLU GLY MET ARG LYS GLN SEQRES 14 A 432 GLY LEU PHE GLN TRP LEU ASP SER LEU GLN ILE ASP ASN SEQRES 15 A 432 LEU THR SER PRO ASP LEU GLN LEU THR VAL GLY ALA VAL SEQRES 16 A 432 ILE VAL GLU GLU MET ARG ALA ALA ILE GLU ARG GLU THR SEQRES 17 A 432 GLY PHE GLN CYS SER ALA GLY ILE SER HIS ASN LYS VAL SEQRES 18 A 432 LEU ALA LYS LEU ALA CYS GLY LEU ASN LYS PRO ASN ARG SEQRES 19 A 432 GLN THR LEU VAL SER HIS GLY SER VAL PRO GLN LEU PHE SEQRES 20 A 432 SER GLN MET PRO ILE ARG LYS ILE ARG SER LEU GLY GLY SEQRES 21 A 432 LYS LEU GLY ALA SER VAL ILE GLU ILE LEU GLY ILE GLU SEQRES 22 A 432 TYR MET GLY GLU LEU THR GLN PHE THR GLU SER GLN LEU SEQRES 23 A 432 GLN SER HIS PHE GLY GLU LYS ASN GLY SER TRP LEU TYR SEQRES 24 A 432 ALA MET CYS ARG GLY ILE GLU HIS ASP PRO VAL LYS PRO SEQRES 25 A 432 ARG GLN LEU PRO LYS THR ILE GLY CYS SER LYS ASN PHE SEQRES 26 A 432 PRO GLY LYS THR ALA LEU ALA THR ARG GLU GLN VAL GLN SEQRES 27 A 432 TRP TRP LEU LEU GLN LEU ALA GLN GLU LEU GLU GLU ARG SEQRES 28 A 432 LEU THR LYS ASP ARG ASN ASP ASN ASP ARG VAL ALA THR SEQRES 29 A 432 GLN LEU VAL VAL SER ILE ARG VAL GLN GLY ASP LYS ARG SEQRES 30 A 432 LEU SER SER LEU ARG ARG CYS CYS ALA LEU THR ARG TYR SEQRES 31 A 432 ASP ALA HIS LYS MET SER HIS ASP ALA PHE THR VAL ILE SEQRES 32 A 432 LYS ASN CYS ASN THR SER GLY ILE GLN THR GLU TRP SER SEQRES 33 A 432 PRO PRO LEU THR MET LEU PHE LEU CYS ALA THR LYS PHE SEQRES 34 A 432 SER ALA SER SEQRES 1 T 12 DC DA DT MF7 DA DT DG DA DC DG DC DT SEQRES 1 P 8 DA DG DC DG DT DC DA DT HET MF7 T 4 24 HET 0KX A 501 28 HET MG A 502 1 HET MG A 503 1 HETNAM MF7 N-{2-AMINO-5-[FORMYL(METHYL)AMINO]-6-HYDROXYPYRIMIDIN- HETNAM 2 MF7 4-YL}-2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO- HETNAM 3 MF7 PENTOFURANOSYLAMINE HETNAM 0KX 2'-DEOXY-5'-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY) HETNAM 2 0KX PHOSPHORYL]AMINO}PHOSPHORYL]CYTIDINE HETNAM MG MAGNESIUM ION FORMUL 2 MF7 C11 H18 N5 O8 P FORMUL 4 0KX C9 H17 N4 O12 P3 FORMUL 5 MG 2(MG 2+) FORMUL 7 HOH *138(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 ARG A 105 1 17 HELIX 6 6 LEU A 121 LYS A 131 1 11 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 SER A 248 1 7 HELIX 13 13 GLN A 249 MET A 250 5 2 HELIX 14 14 PRO A 251 ILE A 255 5 5 HELIX 15 15 GLY A 260 GLY A 271 1 12 HELIX 16 16 TYR A 274 PHE A 281 5 8 HELIX 17 17 THR A 282 GLY A 291 1 10 HELIX 18 18 GLY A 291 CYS A 302 1 12 HELIX 19 19 PRO A 326 ALA A 330 5 5 HELIX 20 20 ARG A 334 ASP A 360 1 27 HELIX 21 21 ASP A 391 VAL A 402 1 12 HELIX 22 22 ILE A 403 ASN A 407 5 5 SHEET 1 A 6 ILE A 109 ARG A 111 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 213 N ASP A 13 SHEET 5 A 6 GLN A 235 LEU A 237 1 O THR A 236 N ALA A 214 SHEET 6 A 6 THR A 145 ILE A 147 1 N TYR A 146 O GLN A 235 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 ALA A 49 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 THR A 427 -1 O ALA A 426 N ILE A 319 SHEET 3 D 3 LEU A 331 THR A 333 -1 N LEU A 331 O LEU A 419 SHEET 1 E 4 ILE A 319 ASN A 324 0 SHEET 2 E 4 GLU A 414 THR A 427 -1 O ALA A 426 N ILE A 319 SHEET 3 E 4 GLN A 365 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 SHEET 1 F 2 ARG A 361 VAL A 362 0 SHEET 2 F 2 SER A 430 ALA A 431 -1 O SER A 430 N VAL A 362 LINK O3' DT T 3 P1 MF7 T 4 1555 1555 1.71 LINK O3' MF7 T 4 P DA T 5 1555 1555 1.59 LINK OD2 ASP A 13 MG MG A 502 1555 1555 1.87 LINK OD1 ASP A 13 MG MG A 503 1555 1555 2.07 LINK O MET A 14 MG MG A 502 1555 1555 2.20 LINK OD2 ASP A 115 MG MG A 502 1555 1555 2.05 LINK OD1 ASP A 115 MG MG A 503 1555 1555 2.19 LINK OE2 GLU A 116 MG MG A 503 1555 1555 2.22 LINK O1B 0KX A 501 MG MG A 502 1555 1555 1.89 LINK O1A 0KX A 501 MG MG A 502 1555 1555 2.13 LINK O3G 0KX A 501 MG MG A 502 1555 1555 2.17 LINK O1A 0KX A 501 MG MG A 503 1555 1555 1.97 LINK MG MG A 503 O HOH A 617 1555 1555 2.28 LINK MG MG A 503 O3' DT P 8 1555 1555 2.33 CISPEP 1 LEU A 150 PRO A 151 0 0.98 CISPEP 2 LYS A 231 PRO A 232 0 4.78 CISPEP 3 SER A 416 PRO A 417 0 -3.13 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 617 SITE 5 AC1 21 HOH A 626 HOH A 663 HOH A 695 DT P 8 SITE 6 AC1 21 MF7 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 617 DT P 8 CRYST1 98.971 98.971 81.624 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 0.010104 0.005834 0.000000 0.00000 SCALE2 0.000000 0.011667 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012251 0.00000