10 20 30 40 50 60 70 80 4AIL - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER TRANSFERASE 10-FEB-12 4AIL
TITLE CRYSTAL STRUCTURE OF AN EVOLVED REPLICATING DNA POLYMERASE
COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*AP*CP*GP*GP*GP*TP*AP*AP*GP*CP*AP)-3'; COMPND 3 CHAIN: A; COMPND 4 MOL_ID: 2; COMPND 5 MOLECULE: 5'-D(*TP*GP*CP*TP*TP*AP*CP*DOCP)-3'; COMPND 6 CHAIN: B; COMPND 7 MOL_ID: 3; COMPND 8 MOLECULE: DNA POLYMERASE; COMPND 9 CHAIN: C; COMPND 10 SYNONYM: PFU POLYMERASE; COMPND 11 EC: 2.7.7.7; COMPND 12 ENGINEERED: YES; COMPND 13 MUTATION: YES
SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 8 ORGANISM_TAXID: 32630; SOURCE 9 MOL_ID: 3; SOURCE 10 ORGANISM_SCIENTIFIC: PYROCOCCUS FURIOSUS; SOURCE 11 ORGANISM_TAXID: 2261; SOURCE 12 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 13 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 14 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 15 EXPRESSION_SYSTEM_VARIANT: STRATAGENE CODON PLUS (RIL); SOURCE 16 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 17 EXPRESSION_SYSTEM_VECTOR: PT7-SC
KEYWDS TRANSFERASE, B FAMILY POLYMERASE, PROTEIN DNA COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR S.A.WYNNE,P.HOLLIGER,A.G.W.LESLIE
REVDAT 2 28-AUG-13 4AIL 1 JRNL REVDAT 1 07-MAR-12 4AIL 0
JRNL AUTH S.A.WYNNE,V.B.PINHEIRO,P.HOLLIGER,A.G.LESLIE JRNL TITL STRUCTURES OF AN APO AND A BINARY COMPLEX OF AN EVOLVED JRNL TITL 2 ARCHEAL B FAMILY DNA POLYMERASE CAPABLE OF SYNTHESISING JRNL TITL 3 HIGHLY CY-DYE LABELLED DNA. JRNL REF PLOS ONE V. 8 70892 2013 JRNL REFN ISSN 1932-6203 JRNL PMID 23940661 JRNL DOI 10.1371/JOURNAL.PONE.0070892
REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH N.RAMSAY,A.JEMTH,A.BROWN,N.CRAMPTON,P.DEAR,P.HOLLIGER REMARK 1 TITL CYDNA: SYNTHESIS AND REPLICATION OF HIGHLY CY-DYE REMARK 1 TITL 2 SUBSTITUTED DNA BY AN EVOLVED POLYMERASE. REMARK 1 REF J.AM.CHEM.SOC. V. 132 5096 2010 REMARK 1 REFN ISSN 0002-7863 REMARK 1 PMID 20235594 REMARK 1 DOI 10.1021/JA909180C
REMARK 2 REMARK 2 RESOLUTION. 2.90 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0002 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 102.82 REMARK 3 DATA CUTOFF (SIGMA(F)) : NONE REMARK 3 COMPLETENESS FOR RANGE (%) : 98.53 REMARK 3 NUMBER OF REFLECTIONS : 25534 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) : 0.22873 REMARK 3 R VALUE (WORKING SET) : 0.22707 REMARK 3 FREE R VALUE : 0.25933 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.0 REMARK 3 FREE R VALUE TEST SET COUNT : 1352 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) : 2.900 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.975 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1751 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.66 REMARK 3 BIN R VALUE (WORKING SET) : 0.364 REMARK 3 BIN FREE R VALUE SET COUNT : 85 REMARK 3 BIN FREE R VALUE : 0.388 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6145 REMARK 3 NUCLEIC ACID ATOMS : 329 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 79 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 72.472 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -3.42 REMARK 3 B22 (A**2) : -2.93 REMARK 3 B33 (A**2) : 6.35 REMARK 3 B12 (A**2) : 0.00 REMARK 3 B13 (A**2) : 0.00 REMARK 3 B23 (A**2) : 0.00 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): 0.390 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.342 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 18.582 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.936 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.912 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6673 ; 0.013 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 4649 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9046 ; 0.825 ; 1.942 REMARK 3 BOND ANGLES OTHERS (DEGREES): 11311 ; 0.768 ; 3.001 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 756 ; 5.202 ; 5.041 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 292 ;27.780 ;23.870 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1187 ;13.406 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 42 ;10.840 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 978 ; 0.125 ; 0.204 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 7019 ; 0.003 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1359 ; 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U REMARK 3 VALUES REFINED INDIVIDUALLY
REMARK 4 REMARK 4 4AIL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 10-FEB-12. REMARK 100 THE PDBE ID CODE IS EBI-51247.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-FEB-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9763 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26919 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.90 REMARK 200 RESOLUTION RANGE LOW (A) : 60.52 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -5.0 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 3.6 REMARK 200 R MERGE (I) : 0.08 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.60 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.06 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.7 REMARK 200 R MERGE FOR SHELL (I) : 0.73 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.00 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 4AHC REMARK 200 REMARK 200 REMARK: NONE
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.04 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM CACODYLATE PH 6.5, 0.1 M REMARK 280 SODIUM CITRATE, 30 % ISOPROPANOL, 10 MM DCTP
REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z 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 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 102.81500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 102.81500 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 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 46.42500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 63.38500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 46.42500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 63.38500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 102.81500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 46.42500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 63.38500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 102.81500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 46.42500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 63.38500 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 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: 3900 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 37060 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -17.2 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 400 REMARK 400 COMPOUND REMARK 400 ENGINEERED RESIDUE IN CHAIN C, VAL 93 TO GLN REMARK 400 ENGINEERED RESIDUE IN CHAIN C, ASP 141 TO ALA REMARK 400 ENGINEERED RESIDUE IN CHAIN C, GLU 143 TO ALA REMARK 400 ENGINEERED RESIDUE IN CHAIN C, VAL 337 TO ILE REMARK 400 ENGINEERED RESIDUE IN CHAIN C, GLU 399 TO ASP REMARK 400 ENGINEERED RESIDUE IN CHAIN C, ASN 400 TO ASP REMARK 400 ENGINEERED RESIDUE IN CHAIN C, ARG 407 TO ILE REMARK 400 ENGINEERED RESIDUE IN CHAIN C, TYR 546 TO HIS
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 DA A 1 REMARK 465 DC A 2 REMARK 465 DG A 3 REMARK 465 LYS C 724 REMARK 465 LYS C 725 REMARK 465 HIS C 726 REMARK 465 LYS C 727 REMARK 465 ASP C 755 REMARK 465 LEU C 756 REMARK 465 ARG C 757 REMARK 465 TYR C 758 REMARK 465 GLN C 759 REMARK 465 LYS C 760 REMARK 465 THR C 761 REMARK 465 ARG C 762 REMARK 465 GLN C 763 REMARK 465 VAL C 764 REMARK 465 GLY C 765 REMARK 465 LEU C 766 REMARK 465 THR C 767 REMARK 465 SER C 768 REMARK 465 TRP C 769 REMARK 465 LEU C 770 REMARK 465 ASN C 771 REMARK 465 ILE C 772 REMARK 465 LYS C 773 REMARK 465 LYS C 774 REMARK 465 SER C 775
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 HOH C 2071 O HOH C 2071 3555 0.59 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 DG A 4 OP3 DG A 4 P -0.118 REMARK 500 DT B 1 OP3 DT B 1 P -0.121 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 LYS C 73 -167.12 -123.85 REMARK 500 ALA C 168 108.16 -165.52 REMARK 500 ASP C 202 71.80 57.31 REMARK 500 TYR C 273 40.68 -108.17 REMARK 500 GLU C 383 129.73 -171.26 REMARK 500 ASP C 400 76.91 33.31 REMARK 500 LYS C 430 -73.91 -55.32 REMARK 500 GLN C 437 -36.27 72.58 REMARK 500 TRP C 505 35.13 -98.52 REMARK 500 CYS C 507 84.23 -151.32 REMARK 500 THR C 542 -67.39 63.64 REMARK 500 LEU C 576 107.74 -57.90 REMARK 500 ASP C 615 21.78 -71.89 REMARK 500 ASP C 636 53.07 -107.39 REMARK 500 GLU C 659 -46.14 68.04 REMARK 500 ILE C 734 -72.78 -90.14 REMARK 500 GLN C 737 -68.36 -147.28 REMARK 500 LYS C 753 88.98 -68.21 REMARK 500 REMARK 500 REMARK: NULL
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2JGU RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF DNA-DIRECTED DNA POLYMERASE REMARK 900 RELATED ID: 4AHC RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF AN EVOLVED REPLICATING DNA REMARK 900 POLYMERASE
DBREF 4AIL A 1 11 PDB 4AIL 4AIL 1 11 DBREF 4AIL B 1 8 PDB 4AIL 4AIL 1 8 DBREF 4AIL C 1 775 UNP P61875 DPOL_PYRFU 1 775
SEQADV 4AIL GLN C 93 UNP P61875 VAL 93 ENGINEERED MUTATION SEQADV 4AIL ALA C 141 UNP P61875 ASP 141 ENGINEERED MUTATION SEQADV 4AIL ALA C 143 UNP P61875 GLU 143 ENGINEERED MUTATION SEQADV 4AIL ILE C 337 UNP P61875 VAL 337 ENGINEERED MUTATION SEQADV 4AIL ASP C 399 UNP P61875 GLU 399 ENGINEERED MUTATION SEQADV 4AIL ASP C 400 UNP P61875 ASN 400 ENGINEERED MUTATION SEQADV 4AIL ILE C 407 UNP P61875 ARG 407 ENGINEERED MUTATION SEQADV 4AIL HIS C 546 UNP P61875 TYR 546 ENGINEERED MUTATION
SEQRES 1 A 11 DA DC DG DG DG DT DA DA DG DC DA SEQRES 1 B 8 DT DG DC DT DT DA DC DOC SEQRES 1 C 775 MET ILE LEU ASP VAL ASP TYR ILE THR GLU GLU GLY LYS SEQRES 2 C 775 PRO VAL ILE ARG LEU PHE LYS LYS GLU ASN GLY LYS PHE SEQRES 3 C 775 LYS ILE GLU HIS ASP ARG THR PHE ARG PRO TYR ILE TYR SEQRES 4 C 775 ALA LEU LEU ARG ASP ASP SER LYS ILE GLU GLU VAL LYS SEQRES 5 C 775 LYS ILE THR GLY GLU ARG HIS GLY LYS ILE VAL ARG ILE SEQRES 6 C 775 VAL ASP VAL GLU LYS VAL GLU LYS LYS PHE LEU GLY LYS SEQRES 7 C 775 PRO ILE THR VAL TRP LYS LEU TYR LEU GLU HIS PRO GLN SEQRES 8 C 775 ASP GLN PRO THR ILE ARG GLU LYS VAL ARG GLU HIS PRO SEQRES 9 C 775 ALA VAL VAL ASP ILE PHE GLU TYR ASP ILE PRO PHE ALA SEQRES 10 C 775 LYS ARG TYR LEU ILE ASP LYS GLY LEU ILE PRO MET GLU SEQRES 11 C 775 GLY GLU GLU GLU LEU LYS ILE LEU ALA PHE ALA ILE ALA SEQRES 12 C 775 THR LEU TYR HIS GLU GLY GLU GLU PHE GLY LYS GLY PRO SEQRES 13 C 775 ILE ILE MET ILE SER TYR ALA ASP GLU ASN GLU ALA LYS SEQRES 14 C 775 VAL ILE THR TRP LYS ASN ILE ASP LEU PRO TYR VAL GLU SEQRES 15 C 775 VAL VAL SER SER GLU ARG GLU MET ILE LYS ARG PHE LEU SEQRES 16 C 775 ARG ILE ILE ARG GLU LYS ASP PRO ASP ILE ILE VAL THR SEQRES 17 C 775 TYR ASN GLY ASP SER PHE ASP PHE PRO TYR LEU ALA LYS SEQRES 18 C 775 ARG ALA GLU LYS LEU GLY ILE LYS LEU THR ILE GLY ARG SEQRES 19 C 775 ASP GLY SER GLU PRO LYS MET GLN ARG ILE GLY ASP MET SEQRES 20 C 775 THR ALA VAL GLU VAL LYS GLY ARG ILE HIS PHE ASP LEU SEQRES 21 C 775 TYR HIS VAL ILE THR ARG THR ILE ASN LEU PRO THR TYR SEQRES 22 C 775 THR LEU GLU ALA VAL TYR GLU ALA ILE PHE GLY LYS PRO SEQRES 23 C 775 LYS GLU LYS VAL TYR ALA ASP GLU ILE ALA LYS ALA TRP SEQRES 24 C 775 GLU SER GLY GLU ASN LEU GLU ARG VAL ALA LYS TYR SER SEQRES 25 C 775 MET GLU ASP ALA LYS ALA THR TYR GLU LEU GLY LYS GLU SEQRES 26 C 775 PHE LEU PRO MET GLU ILE GLN LEU SER ARG LEU ILE GLY SEQRES 27 C 775 GLN PRO LEU TRP ASP VAL SER ARG SER SER THR GLY ASN SEQRES 28 C 775 LEU VAL GLU TRP PHE LEU LEU ARG LYS ALA TYR GLU ARG SEQRES 29 C 775 ASN GLU VAL ALA PRO ASN LYS PRO SER GLU GLU GLU TYR SEQRES 30 C 775 GLN ARG ARG LEU ARG GLU SER TYR THR GLY GLY PHE VAL SEQRES 31 C 775 LYS GLU PRO GLU LYS GLY LEU TRP ASP ASP ILE VAL TYR SEQRES 32 C 775 LEU ASP PHE ILE ALA LEU TYR PRO SER ILE ILE ILE THR SEQRES 33 C 775 HIS ASN VAL SER PRO ASP THR LEU ASN LEU GLU GLY CYS SEQRES 34 C 775 LYS ASN TYR ASP ILE ALA PRO GLN VAL GLY HIS LYS PHE SEQRES 35 C 775 CYS LYS ASP ILE PRO GLY PHE ILE PRO SER LEU LEU GLY SEQRES 36 C 775 HIS LEU LEU GLU GLU ARG GLN LYS ILE LYS THR LYS MET SEQRES 37 C 775 LYS GLU THR GLN ASP PRO ILE GLU LYS ILE LEU LEU ASP SEQRES 38 C 775 TYR ARG GLN LYS ALA ILE LYS LEU LEU ALA ASN SER PHE SEQRES 39 C 775 TYR GLY TYR TYR GLY TYR ALA LYS ALA ARG TRP TYR CYS SEQRES 40 C 775 LYS GLU CYS ALA GLU SER VAL THR ALA TRP GLY ARG LYS SEQRES 41 C 775 TYR ILE GLU LEU VAL TRP LYS GLU LEU GLU GLU LYS PHE SEQRES 42 C 775 GLY PHE LYS VAL LEU TYR ILE ASP THR ASP GLY LEU HIS SEQRES 43 C 775 ALA THR ILE PRO GLY GLY GLU SER GLU GLU ILE LYS LYS SEQRES 44 C 775 LYS ALA LEU GLU PHE VAL LYS TYR ILE ASN SER LYS LEU SEQRES 45 C 775 PRO GLY LEU LEU GLU LEU GLU TYR GLU GLY PHE TYR LYS SEQRES 46 C 775 ARG GLY PHE PHE VAL THR LYS LYS ARG TYR ALA VAL ILE SEQRES 47 C 775 ASP GLU GLU GLY LYS VAL ILE THR ARG GLY LEU GLU ILE SEQRES 48 C 775 VAL ARG ARG ASP TRP SER GLU ILE ALA LYS GLU THR GLN SEQRES 49 C 775 ALA ARG VAL LEU GLU THR ILE LEU LYS HIS GLY ASP VAL SEQRES 50 C 775 GLU GLU ALA VAL ARG ILE VAL LYS GLU VAL ILE GLN LYS SEQRES 51 C 775 LEU ALA ASN TYR GLU ILE PRO PRO GLU LYS LEU ALA ILE SEQRES 52 C 775 TYR GLU GLN ILE THR ARG PRO LEU HIS GLU TYR LYS ALA SEQRES 53 C 775 ILE GLY PRO HIS VAL ALA VAL ALA LYS LYS LEU ALA ALA SEQRES 54 C 775 LYS GLY VAL LYS ILE LYS PRO GLY MET VAL ILE GLY TYR SEQRES 55 C 775 ILE VAL LEU ARG GLY ASP GLY PRO ILE SER ASN ARG ALA SEQRES 56 C 775 ILE LEU ALA GLU GLU TYR ASP PRO LYS LYS HIS LYS TYR SEQRES 57 C 775 ASP ALA GLU TYR TYR ILE GLU ASN GLN VAL LEU PRO ALA SEQRES 58 C 775 VAL LEU ARG ILE LEU GLU GLY PHE GLY TYR ARG LYS GLU SEQRES 59 C 775 ASP LEU ARG TYR GLN LYS THR ARG GLN VAL GLY LEU THR SEQRES 60 C 775 SER TRP LEU ASN ILE LYS LYS SER
MODRES 4AIL DOC B 8 DC 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE
HET DOC B 8 18
HETNAM DOC 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE
FORMUL 2 DOC C9 H14 N3 O6 P FORMUL 3 HOH *79(H2 O)
HELIX 1 1 ASP C 44 SER C 46 5 3 HELIX 2 2 LYS C 47 LYS C 52 1 6 HELIX 3 3 HIS C 89 GLN C 91 5 3 HELIX 4 4 ASP C 92 HIS C 103 1 12 HELIX 5 5 PRO C 115 LYS C 124 1 10 HELIX 6 6 SER C 186 ASP C 202 1 17 HELIX 7 7 PHE C 214 LEU C 226 1 13 HELIX 8 8 LEU C 260 ILE C 268 1 9 HELIX 9 9 THR C 274 PHE C 283 1 10 HELIX 10 10 TYR C 291 GLY C 302 1 12 HELIX 11 11 ASN C 304 GLY C 338 1 35 HELIX 12 12 PRO C 340 SER C 345 1 6 HELIX 13 13 SER C 348 ARG C 364 1 17 HELIX 14 14 SER C 373 ARG C 382 1 10 HELIX 15 15 ALA C 408 HIS C 417 1 10 HELIX 16 16 SER C 420 THR C 423 5 4 HELIX 17 17 GLY C 448 THR C 471 1 24 HELIX 18 18 ILE C 475 ASN C 492 1 18 HELIX 19 19 SER C 493 GLY C 499 1 7 HELIX 20 20 CYS C 507 LYS C 532 1 26 HELIX 21 21 GLU C 553 LEU C 572 1 20 HELIX 22 22 LEU C 609 ARG C 613 5 5 HELIX 23 23 SER C 617 LYS C 633 1 17 HELIX 24 24 ASP C 636 ASN C 653 1 18 HELIX 25 25 PRO C 670 TYR C 674 5 5 HELIX 26 26 GLY C 678 ALA C 689 1 12 HELIX 27 27 ASP C 729 ASN C 736 1 8 HELIX 28 28 GLN C 737 GLU C 747 1 11
SHEET 1 CA 3 ILE C 2 GLU C 10 0 SHEET 2 CA 3 LYS C 13 LYS C 20 -1 O LYS C 13 N GLU C 10 SHEET 3 CA 3 ILE C 28 ASP C 31 -1 O GLU C 29 N LEU C 18 SHEET 1 CB 4 ASP C 67 PHE C 75 0 SHEET 2 CB 4 LYS C 78 TYR C 86 -1 O LYS C 78 N PHE C 75 SHEET 3 CB 4 TYR C 37 LEU C 42 -1 O ILE C 38 N LEU C 85 SHEET 4 CB 4 VAL C 106 PHE C 110 -1 N VAL C 107 O LEU C 41 SHEET 1 CC 2 THR C 55 ARG C 58 0 SHEET 2 CC 2 LYS C 61 ARG C 64 -1 O LYS C 61 N ARG C 58 SHEET 1 CD 6 VAL C 181 VAL C 183 0 SHEET 2 CD 6 ALA C 168 THR C 172 1 O VAL C 170 N GLU C 182 SHEET 3 CD 6 ILE C 157 ALA C 163 -1 O ILE C 160 N ILE C 171 SHEET 4 CD 6 ILE C 137 THR C 144 -1 O ALA C 139 N ALA C 163 SHEET 5 CD 6 ILE C 205 THR C 208 1 O ILE C 205 N LEU C 138 SHEET 6 CD 6 ILE C 256 ASP C 259 1 O ILE C 256 N ILE C 206 SHEET 1 CE 2 LYS C 240 ARG C 243 0 SHEET 2 CE 2 THR C 248 GLU C 251 -1 O ALA C 249 N GLN C 242 SHEET 1 CF 7 VAL C 390 LYS C 391 0 SHEET 2 CF 7 TYR C 539 ASP C 541 -1 O ILE C 540 N LYS C 391 SHEET 3 CF 7 GLY C 544 ALA C 547 -1 O GLY C 544 N ASP C 541 SHEET 4 CF 7 GLY C 396 PHE C 406 -1 O VAL C 402 N ALA C 547 SHEET 5 CF 7 LEU C 578 THR C 591 -1 O GLU C 579 N ASP C 405 SHEET 6 CF 7 ARG C 594 ILE C 598 -1 O ARG C 594 N THR C 591 SHEET 7 CF 7 VAL C 604 ARG C 607 -1 O ILE C 605 N VAL C 597 SHEET 1 CG 2 TYR C 432 ILE C 434 0 SHEET 2 CG 2 LYS C 441 CYS C 443 -1 O PHE C 442 N ASP C 433 SHEET 1 CH 3 ILE C 663 GLN C 666 0 SHEET 2 CH 3 VAL C 699 VAL C 704 -1 O ILE C 700 N GLU C 665 SHEET 3 CH 3 ALA C 715 LEU C 717 -1 O ILE C 716 N ILE C 703
SSBOND 1 CYS C 429 CYS C 443 1555 1555 2.03 SSBOND 2 CYS C 507 CYS C 510 1555 1555 2.05
LINK P DOC B 8 O3' DC B 7 1555 1555 1.60
CRYST1 92.850 126.770 205.630 90.00 90.00 90.00 C 2 2 21 8
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 0.010770 0.000000 0.000000 0.00000
SCALE2 0.000000 0.007888 0.000000 0.00000
SCALE3 0.000000 0.000000 0.004863 0.00000