HEADER LIGASE/DNA 16-FEB-07 2OWO TITLE LAST STOP ON THE ROAD TO REPAIR: STRUCTURE OF E.COLI DNA LIGASE BOUND TITLE 2 TO NICKED DNA-ADENYLATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: 26-MER; COMPND 3 CHAIN: B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 5'-D(*AP*CP*AP*AP*TP*TP*GP*CP*GP*AP*CP*(OMC)P*C)-3'; COMPND 7 CHAIN: C; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: 5'-D(*CP*AP*CP*TP*AP*TP*CP*GP*GP*AP*AP*TP*G)-3'; COMPND 11 CHAIN: D; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 4; COMPND 14 MOLECULE: DNA LIGASE; COMPND 15 CHAIN: A; COMPND 16 SYNONYM: POLYDEOXYRIBONUCLEOTIDE SYNTHASE [NAD+]; COMPND 17 EC: 6.5.1.2; COMPND 18 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: CHEMICALLY SYNTHESIZED; SOURCE 4 MOL_ID: 2; SOURCE 5 SYNTHETIC: YES; SOURCE 6 OTHER_DETAILS: CHEMICALLY SYNTHESIZED; SOURCE 7 MOL_ID: 3; SOURCE 8 SYNTHETIC: YES; SOURCE 9 OTHER_DETAILS: CHEMICALLY SYNTHESIZED; SOURCE 10 MOL_ID: 4; SOURCE 11 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 12 ORGANISM_TAXID: 83333; SOURCE 13 STRAIN: K12; SOURCE 14 GENE: LIGA; SOURCE 15 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 16 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 17 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 18 EXPRESSION_SYSTEM_VECTOR_TYPE: PET16B; SOURCE 19 EXPRESSION_SYSTEM_PLASMID: PET-LIGA KEYWDS DNA, LIGASE, PROTEIN-DNA COMPLEX, LIGASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR S.SHUMAN,J.NANDAKUMAR,P.A.NAIR REVDAT 5 30-AUG-23 2OWO 1 REMARK LINK REVDAT 4 18-OCT-17 2OWO 1 REMARK REVDAT 3 13-JUL-11 2OWO 1 VERSN REVDAT 2 24-FEB-09 2OWO 1 VERSN REVDAT 1 15-MAY-07 2OWO 0 JRNL AUTH J.NANDAKUMAR,P.A.NAIR,S.SHUMAN JRNL TITL LAST STOP ON THE ROAD TO REPAIR: STRUCTURE OF E. COLI DNA JRNL TITL 2 LIGASE BOUND TO NICKED DNA-ADENYLATE. JRNL REF MOL.CELL V. 26 257 2007 JRNL REFN ISSN 1097-2765 JRNL PMID 17466627 JRNL DOI 10.1016/J.MOLCEL.2007.02.026 REMARK 2 REMARK 2 RESOLUTION. 2.30 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.34 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1955275.250 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.4 REMARK 3 NUMBER OF REFLECTIONS : 39098 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) : 0.217 REMARK 3 FREE R VALUE : 0.254 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1959 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.006 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.44 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 88.80 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 5573 REMARK 3 BIN R VALUE (WORKING SET) : 0.2860 REMARK 3 BIN FREE R VALUE : 0.3210 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.20 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 303 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.018 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4565 REMARK 3 NUCLEIC ACID ATOMS : 1062 REMARK 3 HETEROGEN ATOMS : 44 REMARK 3 SOLVENT ATOMS : 320 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 39.40 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.82000 REMARK 3 B22 (A**2) : -0.38000 REMARK 3 B33 (A**2) : 3.20000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 4.85000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.30 REMARK 3 ESD FROM SIGMAA (A) : 0.30 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.37 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.35 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 21.40 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.010 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.340 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.180 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.050 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.060 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.33 REMARK 3 BSOL : 34.03 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 : DNA-RNA-APC_REP.PARAM REMARK 3 PARAMETER FILE 2 : PROTEIN_REP-APL.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : ION.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : DNA-RNA-APC.TOP REMARK 3 TOPOLOGY FILE 2 : PROTEIN-APL.TOP REMARK 3 TOPOLOGY FILE 3 : ION.TOP REMARK 3 TOPOLOGY FILE 4 : WATER.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2OWO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-MAR-07. REMARK 100 THE DEPOSITION ID IS D_1000041677. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-DEC-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 39100 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : 0.08400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.2 REMARK 200 DATA REDUNDANCY IN SHELL : 3.50 REMARK 200 R MERGE FOR SHELL (I) : 0.42200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 1. EFALIGA (AA 71-317 FROM PDB 1TA8) 2. TFILIGA REMARK 200 (AA 433-584 AND 321-391 FROM PDB 1V9P) REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.28 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.52 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: ECOLIGA (0.3 MM) WAS REACTED WITH 5 MM REMARK 280 MGCL2 AND 0.3 MM NAD+ FOR 30 MIN AT 22 C. THE LIGASE- REMARK 280 ADENYLYLATION REACTION WAS THEN QUENCHED BY ADDING 10 MM EDTA. REMARK 280 THE MIXTURE WAS SUPPLEMENTED WITH 26-BP NICKED DUPLEX DNA (0.318 REMARK 280 MM). THIS LIGA-NUCLEIC ACID SOLUTION WAS MIXED 1:2 WITH A WELL REMARK 280 SOLUTION CONTAINING 200 MM AMMONIUM SULFATE, 50 MM SODIUM REMARK 280 ACETATE, 24% PEG-4000. CRYSTALS WERE GROWN AT 22 C BY THE REMARK 280 SITTING DROP VAPOR DIFFUSION METHOD. CRYSTALS APPEARED AFTER 3 REMARK 280 DAYS. THE CRYSTALS WERE TRANSFERRED SERIALLY TO SOLUTIONS REMARK 280 CONTAINING 5% GLYCEROL/24% PEG-4000, 10% GLYCEROL/26% PEG-4000, REMARK 280 15% GLYCEROL/28% PEG-4000, AND 20% GLYCEROL/30% PEG-4000 IN 100 REMARK 280 MM AMMONIUM SULFATE, 50 MM SODIUM ACETATE, AFTER WHICH THEY WERE REMARK 280 FLASH-FROZEN IN LIQUID NITROGEN. , PH 6.0, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 55.22050 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 49.63650 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 55.22050 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 49.63650 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 300 REMARK: BIOLOGICAL ASSEMBLY IS A MONOMER 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, C, D, A 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 706 LIES ON A SPECIAL POSITION. 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 ILE A 587 REMARK 465 VAL A 588 REMARK 465 ILE A 589 REMARK 465 ASN A 590 REMARK 465 ALA A 591 REMARK 465 GLU A 592 REMARK 465 GLU A 593 REMARK 465 ILE A 594 REMARK 465 ASP A 595 REMARK 465 SER A 596 REMARK 465 PRO A 597 REMARK 465 PHE A 598 REMARK 465 ALA A 599 REMARK 465 GLY A 600 REMARK 465 LYS A 601 REMARK 465 THR A 602 REMARK 465 VAL A 603 REMARK 465 VAL A 604 REMARK 465 LEU A 605 REMARK 465 THR A 606 REMARK 465 GLY A 607 REMARK 465 SER A 608 REMARK 465 LEU A 609 REMARK 465 SER A 610 REMARK 465 GLN A 611 REMARK 465 MET A 612 REMARK 465 SER A 613 REMARK 465 ARG A 614 REMARK 465 ASP A 615 REMARK 465 ASP A 616 REMARK 465 ALA A 617 REMARK 465 LYS A 618 REMARK 465 ALA A 619 REMARK 465 ARG A 620 REMARK 465 LEU A 621 REMARK 465 VAL A 622 REMARK 465 GLU A 623 REMARK 465 LEU A 624 REMARK 465 GLY A 625 REMARK 465 ALA A 626 REMARK 465 LYS A 627 REMARK 465 VAL A 628 REMARK 465 ALA A 629 REMARK 465 GLY A 630 REMARK 465 SER A 631 REMARK 465 VAL A 632 REMARK 465 SER A 633 REMARK 465 LYS A 634 REMARK 465 LYS A 635 REMARK 465 THR A 636 REMARK 465 ASP A 637 REMARK 465 LEU A 638 REMARK 465 VAL A 639 REMARK 465 ILE A 640 REMARK 465 ALA A 641 REMARK 465 GLY A 642 REMARK 465 GLU A 643 REMARK 465 ALA A 644 REMARK 465 ALA A 645 REMARK 465 GLY A 646 REMARK 465 SER A 647 REMARK 465 LYS A 648 REMARK 465 LEU A 649 REMARK 465 ALA A 650 REMARK 465 LYS A 651 REMARK 465 ALA A 652 REMARK 465 GLN A 653 REMARK 465 GLU A 654 REMARK 465 LEU A 655 REMARK 465 GLY A 656 REMARK 465 ILE A 657 REMARK 465 GLU A 658 REMARK 465 VAL A 659 REMARK 465 ILE A 660 REMARK 465 ASP A 661 REMARK 465 GLU A 662 REMARK 465 ALA A 663 REMARK 465 GLU A 664 REMARK 465 MET A 665 REMARK 465 LEU A 666 REMARK 465 ARG A 667 REMARK 465 LEU A 668 REMARK 465 LEU A 669 REMARK 465 GLY A 670 REMARK 465 SER A 671 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 PRO A 31 -11.76 -49.15 REMARK 500 SER A 81 -167.03 -108.83 REMARK 500 ARG A 101 -71.31 -68.44 REMARK 500 GLU A 106 -68.15 -2.72 REMARK 500 LYS A 107 81.45 -53.97 REMARK 500 HIS A 160 -31.90 -131.48 REMARK 500 THR A 191 -156.50 -85.76 REMARK 500 VAL A 303 -168.97 -106.49 REMARK 500 THR A 322 -167.91 -168.44 REMARK 500 ALA A 349 53.60 38.71 REMARK 500 HIS A 359 -64.92 65.65 REMARK 500 VAL A 383 -55.49 -140.31 REMARK 500 SER A 413 173.61 -52.87 REMARK 500 ALA A 448 -118.39 -108.87 REMARK 500 THR A 506 -150.36 -131.84 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 DT B 12 0.08 SIDE CHAIN REMARK 500 DG B 13 0.09 SIDE CHAIN 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 ZN A 672 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 408 SG REMARK 620 2 CYS A 411 SG 107.7 REMARK 620 3 CYS A 426 SG 105.8 88.6 REMARK 620 4 CYS A 432 SG 120.8 114.6 114.4 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 672 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 673 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 674 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 675 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 676 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AMP D 53 DBREF 2OWO A 1 671 UNP P15042 DNLJ_ECOLI 1 671 DBREF 2OWO B 1 26 PDB 2OWO 2OWO 1 26 DBREF 2OWO C 27 39 PDB 2OWO 2OWO 27 39 DBREF 2OWO D 40 52 PDB 2OWO 2OWO 40 52 SEQRES 1 B 26 DC DA DT DT DC DC DG DA DT DA DG DT DG SEQRES 2 B 26 DG DG DG DT DC DG DC DA DA DT DT DG DT SEQRES 1 C 13 DA DC DA DA DT DT DG DC DG DA DC OMC DC SEQRES 1 D 13 DC DA DC DT DA DT DC DG DG DA DA DT DG SEQRES 1 A 671 MET GLU SER ILE GLU GLN GLN LEU THR GLU LEU ARG THR SEQRES 2 A 671 THR LEU ARG HIS HIS GLU TYR LEU TYR HIS VAL MET ASP SEQRES 3 A 671 ALA PRO GLU ILE PRO ASP ALA GLU TYR ASP ARG LEU MET SEQRES 4 A 671 ARG GLU LEU ARG GLU LEU GLU THR LYS HIS PRO GLU LEU SEQRES 5 A 671 ILE THR PRO ASP SER PRO THR GLN ARG VAL GLY ALA ALA SEQRES 6 A 671 PRO LEU ALA ALA PHE SER GLN ILE ARG HIS GLU VAL PRO SEQRES 7 A 671 MET LEU SER LEU ASP ASN VAL PHE ASP GLU GLU SER PHE SEQRES 8 A 671 LEU ALA PHE ASN LYS ARG VAL GLN ASP ARG LEU LYS ASN SEQRES 9 A 671 ASN GLU LYS VAL THR TRP CYS CYS GLU LEU LYS LEU ASP SEQRES 10 A 671 GLY LEU ALA VAL SER ILE LEU TYR GLU ASN GLY VAL LEU SEQRES 11 A 671 VAL SER ALA ALA THR ARG GLY ASP GLY THR THR GLY GLU SEQRES 12 A 671 ASP ILE THR SER ASN VAL ARG THR ILE ARG ALA ILE PRO SEQRES 13 A 671 LEU LYS LEU HIS GLY GLU ASN ILE PRO ALA ARG LEU GLU SEQRES 14 A 671 VAL ARG GLY GLU VAL PHE LEU PRO GLN ALA GLY PHE GLU SEQRES 15 A 671 LYS ILE ASN GLU ASP ALA ARG ARG THR GLY GLY LYS VAL SEQRES 16 A 671 PHE ALA ASN PRO ARG ASN ALA ALA ALA GLY SER LEU ARG SEQRES 17 A 671 GLN LEU ASP PRO ARG ILE THR ALA LYS ARG PRO LEU THR SEQRES 18 A 671 PHE PHE CYS TYR GLY VAL GLY VAL LEU GLU GLY GLY GLU SEQRES 19 A 671 LEU PRO ASP THR HIS LEU GLY ARG LEU LEU GLN PHE LYS SEQRES 20 A 671 LYS TRP GLY LEU PRO VAL SER ASP ARG VAL THR LEU CYS SEQRES 21 A 671 GLU SER ALA GLU GLU VAL LEU ALA PHE TYR HIS LYS VAL SEQRES 22 A 671 GLU GLU ASP ARG PRO THR LEU GLY PHE ASP ILE ASP GLY SEQRES 23 A 671 VAL VAL ILE LYS VAL ASN SER LEU ALA GLN GLN GLU GLN SEQRES 24 A 671 LEU GLY PHE VAL ALA ARG ALA PRO ARG TRP ALA VAL ALA SEQRES 25 A 671 PHE LYS PHE PRO ALA GLN GLU GLN MET THR PHE VAL ARG SEQRES 26 A 671 ASP VAL GLU PHE GLN VAL GLY ARG THR GLY ALA ILE THR SEQRES 27 A 671 PRO VAL ALA ARG LEU GLU PRO VAL HIS VAL ALA GLY VAL SEQRES 28 A 671 LEU VAL SER ASN ALA THR LEU HIS ASN ALA ASP GLU ILE SEQRES 29 A 671 GLU ARG LEU GLY LEU ARG ILE GLY ASP LYS VAL VAL ILE SEQRES 30 A 671 ARG ARG ALA GLY ASP VAL ILE PRO GLN VAL VAL ASN VAL SEQRES 31 A 671 VAL LEU SER GLU ARG PRO GLU ASP THR ARG GLU VAL VAL SEQRES 32 A 671 PHE PRO THR HIS CYS PRO VAL CYS GLY SER ASP VAL GLU SEQRES 33 A 671 ARG VAL GLU GLY GLU ALA VAL ALA ARG CYS THR GLY GLY SEQRES 34 A 671 LEU ILE CYS GLY ALA GLN ARG LYS GLU SER LEU LYS HIS SEQRES 35 A 671 PHE VAL SER ARG ARG ALA MET ASP VAL ASP GLY MET GLY SEQRES 36 A 671 ASP LYS ILE ILE ASP GLN LEU VAL GLU LYS GLU TYR VAL SEQRES 37 A 671 HIS THR PRO ALA ASP LEU PHE LYS LEU THR ALA GLY LYS SEQRES 38 A 671 LEU THR GLY LEU GLU ARG MET GLY PRO LYS SER ALA GLN SEQRES 39 A 671 ASN VAL VAL ASN ALA LEU GLU LYS ALA LYS GLU THR THR SEQRES 40 A 671 PHE ALA ARG PHE LEU TYR ALA LEU GLY ILE ARG GLU VAL SEQRES 41 A 671 GLY GLU ALA THR ALA ALA GLY LEU ALA ALA TYR PHE GLY SEQRES 42 A 671 THR LEU GLU ALA LEU GLU ALA ALA SER ILE GLU GLU LEU SEQRES 43 A 671 GLN LYS VAL PRO ASP VAL GLY ILE VAL VAL ALA SER HIS SEQRES 44 A 671 VAL HIS ASN PHE PHE ALA GLU GLU SER ASN ARG ASN VAL SEQRES 45 A 671 ILE SER GLU LEU LEU ALA GLU GLY VAL HIS TRP PRO ALA SEQRES 46 A 671 PRO ILE VAL ILE ASN ALA GLU GLU ILE ASP SER PRO PHE SEQRES 47 A 671 ALA GLY LYS THR VAL VAL LEU THR GLY SER LEU SER GLN SEQRES 48 A 671 MET SER ARG ASP ASP ALA LYS ALA ARG LEU VAL GLU LEU SEQRES 49 A 671 GLY ALA LYS VAL ALA GLY SER VAL SER LYS LYS THR ASP SEQRES 50 A 671 LEU VAL ILE ALA GLY GLU ALA ALA GLY SER LYS LEU ALA SEQRES 51 A 671 LYS ALA GLN GLU LEU GLY ILE GLU VAL ILE ASP GLU ALA SEQRES 52 A 671 GLU MET LEU ARG LEU LEU GLY SER MODRES 2OWO OMC C 38 C O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE HET OMC C 38 21 HET AMP D 53 23 HET ZN A 672 1 HET SO4 A 673 5 HET SO4 A 674 5 HET SO4 A 675 5 HET SO4 A 676 5 HETNAM OMC O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE HETNAM AMP ADENOSINE MONOPHOSPHATE HETNAM ZN ZINC ION HETNAM SO4 SULFATE ION FORMUL 2 OMC C10 H16 N3 O8 P FORMUL 5 AMP C10 H14 N5 O7 P FORMUL 6 ZN ZN 2+ FORMUL 7 SO4 4(O4 S 2-) FORMUL 11 HOH *320(H2 O) HELIX 1 1 SER A 3 MET A 25 1 23 HELIX 2 2 ALA A 33 HIS A 49 1 17 HELIX 3 3 SER A 57 ARG A 61 5 5 HELIX 4 4 ASP A 87 LEU A 102 1 16 HELIX 5 5 ILE A 145 THR A 151 1 7 HELIX 6 6 PRO A 177 THR A 191 1 15 HELIX 7 7 ASN A 198 ARG A 208 1 11 HELIX 8 8 ASP A 211 LYS A 217 1 7 HELIX 9 9 THR A 238 GLY A 250 1 13 HELIX 10 10 SER A 262 ARG A 277 1 16 HELIX 11 11 PRO A 278 LEU A 280 5 3 HELIX 12 12 SER A 293 GLY A 301 1 9 HELIX 13 13 ASN A 360 GLY A 368 1 9 HELIX 14 14 GLY A 381 VAL A 383 5 3 HELIX 15 15 LEU A 392 ARG A 395 5 4 HELIX 16 16 GLY A 428 ILE A 431 5 4 HELIX 17 17 CYS A 432 SER A 445 1 14 HELIX 18 18 GLY A 455 LYS A 465 1 11 HELIX 19 19 THR A 470 LYS A 476 5 7 HELIX 20 20 THR A 478 GLY A 484 1 7 HELIX 21 21 GLY A 489 LYS A 504 1 16 HELIX 22 22 THR A 507 LEU A 515 1 9 HELIX 23 23 GLY A 521 GLY A 533 1 13 HELIX 24 24 THR A 534 ALA A 540 1 7 HELIX 25 25 SER A 542 GLN A 547 1 6 HELIX 26 26 GLY A 553 ALA A 565 1 13 HELIX 27 27 GLU A 566 GLY A 580 1 15 SHEET 1 A 2 GLN A 72 ARG A 74 0 SHEET 2 A 2 THR A 141 GLU A 143 -1 O GLY A 142 N ILE A 73 SHEET 1 B 5 ASP A 83 VAL A 85 0 SHEET 2 B 5 ALA A 310 LYS A 314 1 O ALA A 312 N VAL A 85 SHEET 3 B 5 ILE A 284 VAL A 291 -1 N VAL A 287 O PHE A 313 SHEET 4 B 5 TRP A 110 LEU A 116 -1 N LYS A 115 O GLY A 286 SHEET 5 B 5 THR A 258 CYS A 260 -1 O THR A 258 N CYS A 112 SHEET 1 C 4 VAL A 129 ALA A 134 0 SHEET 2 C 4 LEU A 119 GLU A 126 -1 N LEU A 124 O VAL A 131 SHEET 3 C 4 ARG A 167 PHE A 175 -1 O VAL A 170 N ILE A 123 SHEET 4 C 4 THR A 221 GLU A 231 -1 O GLY A 228 N GLU A 169 SHEET 1 D 5 VAL A 351 THR A 357 0 SHEET 2 D 5 ILE A 337 VAL A 348 -1 N LEU A 343 O SER A 354 SHEET 3 D 5 GLU A 319 VAL A 331 -1 N ASP A 326 O ARG A 342 SHEET 4 D 5 LYS A 374 ALA A 380 -1 O ILE A 377 N GLN A 320 SHEET 5 D 5 ILE A 384 VAL A 390 -1 O ASN A 389 N VAL A 376 SHEET 1 E 2 VAL A 415 ARG A 417 0 SHEET 2 E 2 ALA A 424 CYS A 426 -1 O ARG A 425 N GLU A 416 LINK O3' DC C 37 P OMC C 38 1555 1555 1.60 LINK O3' OMC C 38 P DC C 39 1555 1555 1.59 LINK P DC D 40 O3P AMP D 53 1555 1555 1.60 LINK SG CYS A 408 ZN ZN A 672 1555 1555 2.47 LINK SG CYS A 411 ZN ZN A 672 1555 1555 2.48 LINK SG CYS A 426 ZN ZN A 672 1555 1555 2.47 LINK SG CYS A 432 ZN ZN A 672 1555 1555 2.40 SITE 1 AC1 4 CYS A 408 CYS A 411 CYS A 426 CYS A 432 SITE 1 AC2 5 ARG A 446 ARG A 447 HOH A 922 HOH C 42 SITE 2 AC2 5 DC D 40 SITE 1 AC3 4 ARG A 74 ARG A 510 HOH A 718 HOH A 759 SITE 1 AC4 5 ASN A 95 GLN A 99 SER A 262 ALA A 263 SITE 2 AC4 5 HOH A 799 SITE 1 AC5 2 HIS A 559 ASN A 562 SITE 1 AC6 13 SER A 81 LEU A 82 GLU A 113 LYS A 115 SITE 2 AC6 13 ALA A 120 ARG A 136 GLU A 173 TYR A 225 SITE 3 AC6 13 VAL A 288 LYS A 290 HOH A 752 HOH C 137 SITE 4 AC6 13 DC D 40 CRYST1 110.441 99.273 86.245 90.00 105.33 90.00 C 1 2 1 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 0.009055 0.000000 0.002483 0.00000 SCALE2 0.000000 0.010073 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012023 0.00000