PDB Short entry for 3K5M HEADER TRANSFERASE/DNA 07-OCT-09 3K5M TITLE CRYSTAL STRUCTURE OF E.COLI POL II-ABASIC DNA-DDGTP LT(-2, 2) TERNARY TITLE 2 COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE II; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: POL II; COMPND 5 EC: 2.7.7.7; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: DNA (5'-D(*AP*GP*TP*CP*CP*TP*GP*(3DR) COMPND 10 P*AP*CP*GP*CP*TP*AP*GP*GP*CP*AP*CP*A)-3'); COMPND 11 CHAIN: T; COMPND 12 ENGINEERED: YES; COMPND 13 OTHER_DETAILS: ABASIC LT(-2, 2) TEMPLATE; COMPND 14 MOL_ID: 3; COMPND 15 MOLECULE: DNA (5'-D(*GP*TP*GP*CP*CP*TP*AP*GP*CP*GP*TP*AP*G)-3'); COMPND 16 CHAIN: P; COMPND 17 ENGINEERED: YES; COMPND 18 OTHER_DETAILS: PRIMER SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 STRAIN: K-12; SOURCE 5 GENE: B0060, DINA, JW0059, POLB; 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: MODIFIED PET28; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 MOL_ID: 3; SOURCE 14 SYNTHETIC: YES KEYWDS DNA DAMAGE, DNA REPAIR, DNA-BINDING, DNA-DIRECTED DNA POLYMERASE, KEYWDS 2 NUCLEOTIDYLTRANSFERASE, SOS RESPONSE, TRANSFERASE, TRANSFERASE-DNA KEYWDS 3 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR W.YANG,F.WANG REVDAT 3 06-SEP-23 3K5M 1 REMARK REVDAT 2 13-OCT-21 3K5M 1 REMARK SEQADV LINK REVDAT 1 02-FEB-10 3K5M 0 JRNL AUTH F.WANG,W.YANG JRNL TITL STRUCTURAL INSIGHT INTO TRANSLESION SYNTHESIS BY DNA POL II. JRNL REF CELL(CAMBRIDGE,MASS.) V. 139 1279 2009 JRNL REFN ISSN 0092-8674 JRNL PMID 20064374 JRNL DOI 10.1016/J.CELL.2009.11.043 REMARK 2 REMARK 2 RESOLUTION. 2.04 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.04 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.43 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 88.7 REMARK 3 NUMBER OF REFLECTIONS : 57663 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 SET) : 0.243 REMARK 3 FREE R VALUE : 0.260 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.200 REMARK 3 FREE R VALUE TEST SET COUNT : 1450 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.04 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.11 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.3090 REMARK 3 BIN FREE R VALUE : 0.3190 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 132 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6204 REMARK 3 NUCLEIC ACID ATOMS : 663 REMARK 3 HETEROGEN ATOMS : 32 REMARK 3 SOLVENT ATOMS : 491 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.13 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 5.75900 REMARK 3 B22 (A**2) : -2.91800 REMARK 3 B33 (A**2) : -2.84100 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.29 REMARK 3 ESD FROM SIGMAA (A) : 0.23 REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.32 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.29 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.013 REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.212 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.825 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.792 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.536 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 51.78 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : CNS_TOPPAR:PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : CNS_TOPPAR:DNA-RNA_REP.PARAM REMARK 3 PARAMETER FILE 3 : CNS_TOPPAR:WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : CNS_TOPPAR:ION.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : CNS_TOPPAR:PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : CNS_TOPPAR:DNA-RNA.TOP REMARK 3 TOPOLOGY FILE 3 : CNS_TOPPAR:WATER.TOP REMARK 3 TOPOLOGY FILE 4 : CNS_TOPPAR:ION.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3K5M COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-OCT-09. REMARK 100 THE DEPOSITION ID IS D_1000055575. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-JAN-08 REMARK 200 TEMPERATURE (KELVIN) : 95 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 62414 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.040 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 (%) : 95.8 REMARK 200 DATA REDUNDANCY : 4.100 REMARK 200 R MERGE (I) : 0.07300 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.6000 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) : 2.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.7 REMARK 200 DATA REDUNDANCY IN SHELL : 4.20 REMARK 200 R MERGE FOR SHELL (I) : 0.50000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.100 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: PDB ENTRY 3K59 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.95 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.51 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20-25% PEGMME3350, 0.1 M AMMONIUM REMARK 280 FORMATE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 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 36.55450 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 72.36750 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 47.61400 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 72.36750 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 36.55450 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 47.61400 REMARK 290 SMTRY3 4 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: 7200 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 37160 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -43.0 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 GLY A -2 REMARK 465 GLY A 259 REMARK 465 PHE A 260 REMARK 465 VAL A 264 REMARK 465 LYS A 305 REMARK 465 ASN A 771 REMARK 465 PHE A 772 REMARK 465 ALA A 773 REMARK 465 THR A 774 REMARK 465 LEU A 775 REMARK 465 MET A 776 REMARK 465 THR A 777 REMARK 465 GLY A 778 REMARK 465 GLN A 779 REMARK 465 LEU A 780 REMARK 465 GLY A 781 REMARK 465 LEU A 782 REMARK 465 PHE A 783 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 THR A 27 CB OG1 CG2 REMARK 470 ASN A 132 CB CG OD1 ND2 REMARK 470 GLU A 294 CG CD OE1 OE2 REMARK 470 ILE A 307 CG1 CG2 CD1 REMARK 470 THR A 340 OG1 CG2 REMARK 470 LYS A 672 CG CD CE NZ REMARK 470 GLU A 677 CG CD OE1 OE2 REMARK 470 ARG A 697 CB CG CD NE CZ NH1 NH2 REMARK 470 GLN A 758 CG CD OE1 NE2 REMARK 470 GLU A 762 CG CD OE1 OE2 REMARK 470 GLU A 769 CB CG CD OE1 OE2 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 DA T 818 P DA T 818 O5' -0.068 REMARK 500 DA T 818 O4' DA T 818 C4' -0.070 REMARK 500 DA T 818 C1' DA T 818 N9 -0.109 REMARK 500 DA T 818 C2 DA T 818 N3 -0.056 REMARK 500 DA T 818 N3 DA T 818 C4 -0.040 REMARK 500 DA T 818 C4 DA T 818 C5 -0.045 REMARK 500 DA T 818 C5 DA T 818 C6 -0.088 REMARK 500 DA T 818 N7 DA T 818 C8 -0.043 REMARK 500 DA T 818 N9 DA T 818 C4 -0.049 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 DA T 799 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 DC T 817 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 DA T 818 O3' - P - OP2 ANGL. DEV. = 7.6 DEGREES REMARK 500 DA T 818 O4' - C1' - N9 ANGL. DEV. = -16.6 DEGREES REMARK 500 DG P 903 O5' - P - OP2 ANGL. DEV. = -7.3 DEGREES REMARK 500 DC P 904 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 DG P 913 O4' - C1' - N9 ANGL. DEV. = 2.5 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 121 -85.97 -112.00 REMARK 500 PHE A 228 -70.07 -102.26 REMARK 500 ILE A 307 63.75 33.44 REMARK 500 SER A 414 84.37 55.21 REMARK 500 THR A 546 -64.97 62.43 REMARK 500 TYR A 662 -12.30 -140.36 REMARK 500 ARG A 725 152.12 77.94 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 CA A1001 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 419 OD2 REMARK 620 2 TYR A 420 O 79.7 REMARK 620 3 ASP A 547 OD2 89.3 88.5 REMARK 620 4 DG3 A 914 O1G 80.8 97.2 167.5 REMARK 620 5 DG3 A 914 O1B 95.9 170.7 99.6 73.9 REMARK 620 6 DG3 A 914 O1A 164.2 86.4 97.7 93.8 96.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A1002 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 419 OD1 REMARK 620 2 ASP A 547 OD1 72.6 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DG3 A 914 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 1002 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3K57 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF E.COLI POL II-NORMAL DNA-DATP TERNARY COMPLEX REMARK 900 RELATED ID: 3K58 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF E.COLI POL II-NORMAL DNA-DTTP TERNARY COMPLEX REMARK 900 RELATED ID: 3K59 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF E.COLI POL II-NORMAL DNA-DCTP TERNARY COMPLEX REMARK 900 RELATED ID: 3K5A RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF E.COLI POL II-NORMAL DNA-DGTP TERNARY COMPLEX REMARK 900 RELATED ID: 3K5L RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF E.COLI POL II-ABASIC DNA-DATP LT(0, 3) TERNARY REMARK 900 COMPLEX REMARK 900 RELATED ID: 3K5N RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF E.COLI POL II-ABASIC DNA BINARY COMPLEX REMARK 900 RELATED ID: 3K5O RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF E.COLI POL II DBREF 3K5M A 1 783 UNP P21189 DPO2_ECOLI 1 783 DBREF 3K5M T 799 818 PDB 3K5M 3K5M 799 818 DBREF 3K5M P 901 913 PDB 3K5M 3K5M 901 913 SEQADV 3K5M GLY A -2 UNP P21189 EXPRESSION TAG SEQADV 3K5M PRO A -1 UNP P21189 EXPRESSION TAG SEQADV 3K5M HIS A 0 UNP P21189 EXPRESSION TAG SEQADV 3K5M ASN A 335 UNP P21189 ASP 335 ENGINEERED MUTATION SEQRES 1 A 786 GLY PRO HIS MET ALA GLN ALA GLY PHE ILE LEU THR ARG SEQRES 2 A 786 HIS TRP ARG ASP THR PRO GLN GLY THR GLU VAL SER PHE SEQRES 3 A 786 TRP LEU ALA THR ASP ASN GLY PRO LEU GLN VAL THR LEU SEQRES 4 A 786 ALA PRO GLN GLU SER VAL ALA PHE ILE PRO ALA ASP GLN SEQRES 5 A 786 VAL PRO ARG ALA GLN HIS ILE LEU GLN GLY GLU GLN GLY SEQRES 6 A 786 PHE ARG LEU THR PRO LEU ALA LEU LYS ASP PHE HIS ARG SEQRES 7 A 786 GLN PRO VAL TYR GLY LEU TYR CYS ARG ALA HIS ARG GLN SEQRES 8 A 786 LEU MET ASN TYR GLU LYS ARG LEU ARG GLU GLY GLY VAL SEQRES 9 A 786 THR VAL TYR GLU ALA ASP VAL ARG PRO PRO GLU ARG TYR SEQRES 10 A 786 LEU MET GLU ARG PHE ILE THR SER PRO VAL TRP VAL GLU SEQRES 11 A 786 GLY ASP MET HIS ASN GLY THR ILE VAL ASN ALA ARG LEU SEQRES 12 A 786 LYS PRO HIS PRO ASP TYR ARG PRO PRO LEU LYS TRP VAL SEQRES 13 A 786 SER ILE ASP ILE GLU THR THR ARG HIS GLY GLU LEU TYR SEQRES 14 A 786 CYS ILE GLY LEU GLU GLY CYS GLY GLN ARG ILE VAL TYR SEQRES 15 A 786 MET LEU GLY PRO GLU ASN GLY ASP ALA SER SER LEU ASP SEQRES 16 A 786 PHE GLU LEU GLU TYR VAL ALA SER ARG PRO GLN LEU LEU SEQRES 17 A 786 GLU LYS LEU ASN ALA TRP PHE ALA ASN TYR ASP PRO ASP SEQRES 18 A 786 VAL ILE ILE GLY TRP ASN VAL VAL GLN PHE ASP LEU ARG SEQRES 19 A 786 MET LEU GLN LYS HIS ALA GLU ARG TYR ARG LEU PRO LEU SEQRES 20 A 786 ARG LEU GLY ARG ASP ASN SER GLU LEU GLU TRP ARG GLU SEQRES 21 A 786 HIS GLY PHE LYS ASN GLY VAL PHE PHE ALA GLN ALA LYS SEQRES 22 A 786 GLY ARG LEU ILE ILE ASP GLY ILE GLU ALA LEU LYS SER SEQRES 23 A 786 ALA PHE TRP ASN PHE SER SER PHE SER LEU GLU THR VAL SEQRES 24 A 786 ALA GLN GLU LEU LEU GLY GLU GLY LYS SER ILE ASP ASN SEQRES 25 A 786 PRO TRP ASP ARG MET ASP GLU ILE ASP ARG ARG PHE ALA SEQRES 26 A 786 GLU ASP LYS PRO ALA LEU ALA THR TYR ASN LEU LYS ASN SEQRES 27 A 786 CYS GLU LEU VAL THR GLN ILE PHE HIS LYS THR GLU ILE SEQRES 28 A 786 MET PRO PHE LEU LEU GLU ARG ALA THR VAL ASN GLY LEU SEQRES 29 A 786 PRO VAL ASP ARG HIS GLY GLY SER VAL ALA ALA PHE GLY SEQRES 30 A 786 HIS LEU TYR PHE PRO ARG MET HIS ARG ALA GLY TYR VAL SEQRES 31 A 786 ALA PRO ASN LEU GLY GLU VAL PRO PRO HIS ALA SER PRO SEQRES 32 A 786 GLY GLY TYR VAL MET ASP SER ARG PRO GLY LEU TYR ASP SEQRES 33 A 786 SER VAL LEU VAL LEU ASP TYR LYS SER LEU TYR PRO SER SEQRES 34 A 786 ILE ILE ARG THR PHE LEU ILE ASP PRO VAL GLY LEU VAL SEQRES 35 A 786 GLU GLY MET ALA GLN PRO ASP PRO GLU HIS SER THR GLU SEQRES 36 A 786 GLY PHE LEU ASP ALA TRP PHE SER ARG GLU LYS HIS CYS SEQRES 37 A 786 LEU PRO GLU ILE VAL THR ASN ILE TRP HIS GLY ARG ASP SEQRES 38 A 786 GLU ALA LYS ARG GLN GLY ASN LYS PRO LEU SER GLN ALA SEQRES 39 A 786 LEU LYS ILE ILE MET ASN ALA PHE TYR GLY VAL LEU GLY SEQRES 40 A 786 THR THR ALA CYS ARG PHE PHE ASP PRO ARG LEU ALA SER SEQRES 41 A 786 SER ILE THR MET ARG GLY HIS GLN ILE MET ARG GLN THR SEQRES 42 A 786 LYS ALA LEU ILE GLU ALA GLN GLY TYR ASP VAL ILE TYR SEQRES 43 A 786 GLY ASP THR ASP SER THR PHE VAL TRP LEU LYS GLY ALA SEQRES 44 A 786 HIS SER GLU GLU GLU ALA ALA LYS ILE GLY ARG ALA LEU SEQRES 45 A 786 VAL GLN HIS VAL ASN ALA TRP TRP ALA GLU THR LEU GLN SEQRES 46 A 786 LYS GLN ARG LEU THR SER ALA LEU GLU LEU GLU TYR GLU SEQRES 47 A 786 THR HIS PHE CYS ARG PHE LEU MET PRO THR ILE ARG GLY SEQRES 48 A 786 ALA ASP THR GLY SER LYS LYS ARG TYR ALA GLY LEU ILE SEQRES 49 A 786 GLN GLU GLY ASP LYS GLN ARG MET VAL PHE LYS GLY LEU SEQRES 50 A 786 GLU THR VAL ARG THR ASP TRP THR PRO LEU ALA GLN GLN SEQRES 51 A 786 PHE GLN GLN GLU LEU TYR LEU ARG ILE PHE ARG ASN GLU SEQRES 52 A 786 PRO TYR GLN GLU TYR VAL ARG GLU THR ILE ASP LYS LEU SEQRES 53 A 786 MET ALA GLY GLU LEU ASP ALA ARG LEU VAL TYR ARG LYS SEQRES 54 A 786 ARG LEU ARG ARG PRO LEU SER GLU TYR GLN ARG ASN VAL SEQRES 55 A 786 PRO PRO HIS VAL ARG ALA ALA ARG LEU ALA ASP GLU GLU SEQRES 56 A 786 ASN GLN LYS ARG GLY ARG PRO LEU GLN TYR GLN ASN ARG SEQRES 57 A 786 GLY THR ILE LYS TYR VAL TRP THR THR ASN GLY PRO GLU SEQRES 58 A 786 PRO LEU ASP TYR GLN ARG SER PRO LEU ASP TYR GLU HIS SEQRES 59 A 786 TYR LEU THR ARG GLN LEU GLN PRO VAL ALA GLU GLY ILE SEQRES 60 A 786 LEU PRO PHE ILE GLU ASP ASN PHE ALA THR LEU MET THR SEQRES 61 A 786 GLY GLN LEU GLY LEU PHE SEQRES 1 T 20 DA DG DT DC DC DT DG 3DR DA DC DG DC DT SEQRES 2 T 20 DA DG DG DC DA DC DA SEQRES 1 P 13 DG DT DG DC DC DT DA DG DC DG DT DA DG HET 3DR T 806 11 HET DG3 A 914 30 HET CA A1001 1 HET CA A1002 1 HETNAM 3DR 1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE HETNAM DG3 2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE HETNAM CA CALCIUM ION HETSYN 3DR ABASIC DIDEOXYRIBOSE FORMUL 2 3DR C5 H11 O6 P FORMUL 4 DG3 C10 H16 N5 O12 P3 FORMUL 5 CA 2(CA 2+) FORMUL 7 HOH *491(H2 O) HELIX 1 1 GLN A 49 LEU A 57 1 9 HELIX 2 2 ALA A 85 GLY A 99 1 15 HELIX 3 3 ARG A 109 ARG A 118 1 10 HELIX 4 4 SER A 200 ASP A 216 1 17 HELIX 5 5 PHE A 228 ARG A 241 1 14 HELIX 6 6 GLY A 277 ALA A 284 1 8 HELIX 7 7 SER A 292 GLY A 302 1 11 HELIX 8 8 ASN A 309 ASP A 324 1 16 HELIX 9 9 ASP A 324 GLU A 347 1 24 HELIX 10 10 GLU A 347 GLY A 360 1 14 HELIX 11 11 GLY A 368 ALA A 384 1 17 HELIX 12 12 SER A 422 LEU A 432 1 11 HELIX 13 13 ASP A 434 GLN A 444 1 11 HELIX 14 14 CYS A 465 GLY A 484 1 20 HELIX 15 15 ASN A 485 GLY A 504 1 20 HELIX 16 16 ASP A 512 ALA A 536 1 25 HELIX 17 17 SER A 558 LYS A 583 1 26 HELIX 18 18 LEU A 634 ARG A 638 5 5 HELIX 19 19 THR A 642 ARG A 658 1 17 HELIX 20 20 TYR A 662 ALA A 675 1 14 HELIX 21 21 LEU A 678 LEU A 682 5 5 HELIX 22 22 PRO A 691 TYR A 695 5 5 HELIX 23 23 PRO A 700 GLY A 717 1 18 HELIX 24 24 ASP A 748 GLN A 756 1 9 HELIX 25 25 GLN A 756 LEU A 765 1 10 HELIX 26 26 PRO A 766 GLU A 769 5 4 SHEET 1 A 6 HIS A 0 ARG A 13 0 SHEET 2 A 6 GLU A 20 THR A 27 -1 O GLU A 20 N ARG A 13 SHEET 3 A 6 GLY A 30 LEU A 36 -1 O VAL A 34 N PHE A 23 SHEET 4 A 6 THR A 134 PRO A 142 1 O ILE A 135 N THR A 35 SHEET 5 A 6 PRO A 123 HIS A 131 -1 N HIS A 131 O THR A 134 SHEET 6 A 6 HIS A 0 ARG A 13 -1 N GLN A 3 O VAL A 126 SHEET 1 B 3 SER A 41 PRO A 46 0 SHEET 2 B 3 PRO A 77 CYS A 83 -1 O LEU A 81 N ALA A 43 SHEET 3 B 3 PHE A 63 LYS A 71 -1 N THR A 66 O GLY A 80 SHEET 1 C 6 GLU A 194 VAL A 198 0 SHEET 2 C 6 GLN A 175 LEU A 181 1 N MET A 180 O GLU A 196 SHEET 3 C 6 LEU A 165 GLY A 172 -1 N LEU A 170 O ILE A 177 SHEET 4 C 6 TRP A 152 THR A 159 -1 N SER A 154 O GLU A 171 SHEET 5 C 6 VAL A 219 GLY A 222 1 O ILE A 221 N VAL A 153 SHEET 6 C 6 LEU A 273 ASP A 276 1 O LEU A 273 N ILE A 220 SHEET 1 D 2 GLU A 254 ARG A 256 0 SHEET 2 D 2 PHE A 266 GLN A 268 -1 O PHE A 266 N ARG A 256 SHEET 1 E 6 ASP A 540 ASP A 545 0 SHEET 2 E 6 SER A 548 TRP A 552 -1 O PHE A 550 N TYR A 543 SHEET 3 E 6 GLY A 410 TYR A 420 -1 N LEU A 416 O VAL A 551 SHEET 4 E 6 LEU A 592 MET A 603 -1 O MET A 603 N GLY A 410 SHEET 5 E 6 TYR A 617 GLN A 622 -1 O ALA A 618 N LEU A 602 SHEET 6 E 6 GLN A 627 LYS A 632 -1 O LYS A 632 N TYR A 617 SHEET 1 F 2 SER A 450 GLU A 452 0 SHEET 2 F 2 TRP A 458 SER A 460 -1 O PHE A 459 N THR A 451 SHEET 1 G 3 TYR A 684 LEU A 688 0 SHEET 2 G 3 GLY A 726 THR A 733 -1 O GLY A 726 N LEU A 688 SHEET 3 G 3 GLY A 736 PRO A 739 -1 O GLU A 738 N VAL A 731 LINK O3' DG T 805 P 3DR T 806 1555 1555 1.60 LINK O3' 3DR T 806 P DA T 807 1555 1555 1.60 LINK OD2 ASP A 419 CA CA A1001 1555 1555 2.42 LINK OD1 ASP A 419 CA CA A1002 1555 1555 2.82 LINK O TYR A 420 CA CA A1001 1555 1555 2.51 LINK OD2 ASP A 547 CA CA A1001 1555 1555 1.85 LINK OD1 ASP A 547 CA CA A1002 1555 1555 2.92 LINK O1G DG3 A 914 CA CA A1001 1555 1555 2.31 LINK O1B DG3 A 914 CA CA A1001 1555 1555 2.50 LINK O1A DG3 A 914 CA CA A1001 1555 1555 2.53 CISPEP 1 GLY A 182 PRO A 183 0 0.70 SITE 1 AC1 20 ASP A 419 TYR A 420 LYS A 421 SER A 422 SITE 2 AC1 20 LEU A 423 ARG A 477 LYS A 493 ASN A 497 SITE 3 AC1 20 TYR A 500 ASP A 547 HOH A 826 HOH A 865 SITE 4 AC1 20 HOH A 930 HOH A 957 CA A1001 CA A1002 SITE 5 AC1 20 HOH A1115 DG P 913 DC T 802 DC T 803 SITE 1 AC2 4 ASP A 419 TYR A 420 ASP A 547 DG3 A 914 SITE 1 AC3 4 ASP A 419 ASP A 547 DG3 A 914 DG P 913 CRYST1 73.109 95.228 144.735 90.00 90.00 90.00 P 21 21 21 4 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 0.013678 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010501 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006909 0.00000