HEADER LIGASE/LIGASE INHIBITOR/DNA 15-AUG-12 4GLX TITLE DNA LIGASE A IN COMPLEX WITH INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (26-MER); COMPND 3 CHAIN: B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (5'-D(*AP*CP*AP*AP*TP*TP*GP*CP*GP*AP*CP*CP*C)-3'); COMPND 7 CHAIN: C; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: DNA (5'-D(P*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 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_COMMON: SYNTHETIC CONSTRUCT; SOURCE 5 ORGANISM_TAXID: 32630; SOURCE 6 MOL_ID: 2; SOURCE 7 SYNTHETIC: YES; SOURCE 8 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 9 ORGANISM_COMMON: SYNTHETIC CONSTRUCT; SOURCE 10 ORGANISM_TAXID: 32630; SOURCE 11 MOL_ID: 3; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 14 ORGANISM_COMMON: SYNTHETIC CONSTRUCT; SOURCE 15 ORGANISM_TAXID: 32630; SOURCE 16 MOL_ID: 4; SOURCE 17 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 18 ORGANISM_TAXID: 83333; SOURCE 19 STRAIN: K12; SOURCE 20 GENE: B2411, DNAL, JW2403, LIG, LIGA, LOP, PDEC; SOURCE 21 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 22 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS DNA LIGASE A, INHIBITOR, LIGASE-LIGASE INHIBITOR-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR L.PRADE,R.LANGE,N.TIDTEN-LUKSCH,A.CHAMBOVEY REVDAT 4 28-FEB-24 4GLX 1 REMARK LINK REVDAT 3 15-NOV-17 4GLX 1 REMARK REVDAT 2 31-OCT-12 4GLX 1 JRNL REVDAT 1 10-OCT-12 4GLX 0 JRNL AUTH J.P.SURIVET,R.LANGE,C.HUBSCHWERLEN,W.KECK,J.L.SPECKLIN, JRNL AUTH 2 D.RITZ,D.BUR,H.LOCHER,P.SEILER,D.S.STRASSER,L.PRADE,C.KOHL, JRNL AUTH 3 C.SCHMITT,G.CHAPOUX,E.ILHAN,N.EKAMBARAM,A.ATHANASIOU, JRNL AUTH 4 A.KNEZEVIC,D.SABATO,A.CHAMBOVEY,M.GAERTNER,M.ENDERLIN, JRNL AUTH 5 M.BOEHME,V.SIPPEL,P.WYSS JRNL TITL STRUCTURE-GUIDED DESIGN, SYNTHESIS AND BIOLOGICAL EVALUATION JRNL TITL 2 OF NOVEL DNA LIGASE INHIBITORS WITH IN VITRO AND IN VIVO JRNL TITL 3 ANTI-STAPHYLOCOCCAL ACTIVITY. JRNL REF BIOORG.MED.CHEM.LETT. V. 22 6705 2012 JRNL REFN ISSN 0960-894X JRNL PMID 23006603 JRNL DOI 10.1016/J.BMCL.2012.08.094 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0117 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.73 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 62.7 REMARK 3 NUMBER OF REFLECTIONS : 45003 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) : 0.203 REMARK 3 R VALUE (WORKING SET) : 0.201 REMARK 3 FREE R VALUE : 0.250 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2251 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) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.95 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1432 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 28.81 REMARK 3 BIN R VALUE (WORKING SET) : 0.2790 REMARK 3 BIN FREE R VALUE SET COUNT : 76 REMARK 3 BIN FREE R VALUE : 0.3260 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4308 REMARK 3 NUCLEIC ACID ATOMS : 1061 REMARK 3 HETEROGEN ATOMS : 25 REMARK 3 SOLVENT ATOMS : 204 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.81 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.24 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.18000 REMARK 3 B22 (A**2) : 0.53000 REMARK 3 B33 (A**2) : -0.13000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.42000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.240 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.205 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.107 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.668 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.909 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.862 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5645 ; 0.017 ; 0.018 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7908 ; 2.090 ; 1.829 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 572 ; 6.542 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 189 ;32.812 ;23.228 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 685 ;17.583 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 38 ;18.914 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 862 ; 0.130 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3930 ; 0.012 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER 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: NULL REMARK 4 REMARK 4 4GLX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-AUG-12. REMARK 100 THE DEPOSITION ID IS D_1000074348. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-MAY-09 REMARK 200 TEMPERATURE (KELVIN) : 113 REMARK 200 PH : 5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06DA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : BARTELS MONOCHROMATOR WITH DUAL REMARK 200 CHANNEL CUT CRYSTALS (DCCM) IN (+ REMARK 200 --+) GEOMETRY REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR225 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : INTEGRATE REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 19.730 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.1 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.15900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.2200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.10 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.4 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.64900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.040 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.09 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.87 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM CITRATE, 25 MM SODIUM REMARK 280 ACETATE, 24 % (W/V) PEG 4000, 0.2 M AMMONIUM SULFATE, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 291.15K, PH 5 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 55.49500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 50.07000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 55.49500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 50.07000 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 8810 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 31230 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -69.0 KCAL/MOL 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 703 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 MET A 1 REMARK 465 GLU A 2 REMARK 465 VAL A 62 REMARK 465 GLY A 63 REMARK 465 ALA A 64 REMARK 465 ALA A 65 REMARK 465 LEU A 102 REMARK 465 LYS A 103 REMARK 465 ASN A 104 REMARK 465 ASN A 105 REMARK 465 GLU A 106 REMARK 465 LYS A 107 REMARK 465 VAL A 108 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 SER A 3 OG REMARK 470 GLU A 5 CG CD OE1 OE2 REMARK 470 GLN A 6 CG CD OE1 NE2 REMARK 470 GLN A 7 CG CD OE1 NE2 REMARK 470 ASP A 26 CG OD1 OD2 REMARK 470 GLU A 34 CG CD OE1 OE2 REMARK 470 LYS A 48 CG CD CE NZ REMARK 470 GLN A 60 CG CD OE1 NE2 REMARK 470 ARG A 61 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 76 CG CD OE1 OE2 REMARK 470 GLU A 89 CG CD OE1 OE2 REMARK 470 LYS A 96 CG CD CE NZ REMARK 470 VAL A 98 CG1 CG2 REMARK 470 ASP A 100 CG OD1 OD2 REMARK 470 ARG A 101 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 158 CG CD CE NZ REMARK 470 ARG A 190 CG CD NE CZ NH1 NH2 REMARK 470 THR A 191 OG1 CG2 REMARK 470 VAL A 227 CG1 CG2 REMARK 470 LYS A 248 CG CD CE NZ REMARK 470 ASP A 255 CG OD1 OD2 REMARK 470 GLU A 261 CG CD OE1 OE2 REMARK 470 GLU A 298 CG CD OE1 OE2 REMARK 470 GLN A 299 CG CD OE1 NE2 REMARK 470 PHE A 302 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ARG A 305 CG CD NE CZ NH1 NH2 REMARK 470 ASP A 398 CG OD1 OD2 REMARK 470 ARG A 400 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 416 CG CD OE1 OE2 REMARK 470 VAL A 418 CG1 CG2 REMARK 470 GLU A 419 CG CD OE1 OE2 REMARK 470 ILE A 431 CG1 CG2 CD1 REMARK 470 LYS A 441 CG CD CE NZ REMARK 470 HIS A 469 CG ND1 CD2 CE1 NE2 REMARK 470 GLU A 486 CG CD OE1 OE2 REMARK 470 LYS A 491 CG CD CE NZ REMARK 470 LYS A 502 CG CD CE NZ REMARK 470 GLU A 544 CG CD OE1 OE2 REMARK 470 GLU A 545 CG CD OE1 OE2 REMARK 470 GLU A 566 CG CD OE1 OE2 REMARK 470 GLU A 567 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 DC D 40 P DC D 40 OP3 -0.122 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 DC B 5 C3' - O3' - P ANGL. DEV. = 9.3 DEGREES REMARK 500 DA B 21 C3' - O3' - P ANGL. DEV. = 9.0 DEGREES REMARK 500 DA B 22 O3' - P - O5' ANGL. DEV. = -16.7 DEGREES REMARK 500 DT B 24 C3' - O3' - P ANGL. DEV. = 7.9 DEGREES REMARK 500 DG B 25 C3' - O3' - P ANGL. DEV. = 11.2 DEGREES REMARK 500 DC C 28 C3' - O3' - P ANGL. DEV. = 7.2 DEGREES REMARK 500 DA C 29 C3' - O3' - P ANGL. DEV. = 8.3 DEGREES REMARK 500 DT C 32 C3' - O3' - P ANGL. DEV. = 8.5 DEGREES REMARK 500 DC C 37 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 DC C 37 C3' - O3' - P ANGL. DEV. = 10.8 DEGREES REMARK 500 DG D 47 C3' - O3' - P ANGL. DEV. = 7.5 DEGREES REMARK 500 DG D 48 C3' - O3' - P ANGL. DEV. = 7.7 DEGREES REMARK 500 ARG A 40 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 ARG A 40 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 ARG A 342 NE - CZ - NH1 ANGL. DEV. = 4.6 DEGREES REMARK 500 ARG A 342 NE - CZ - NH2 ANGL. DEV. = -4.6 DEGREES REMARK 500 LYS A 374 CD - CE - NZ ANGL. DEV. = -18.9 DEGREES REMARK 500 LEU A 500 CA - CB - CG ANGL. DEV. = 16.8 DEGREES REMARK 500 LEU A 500 CB - CG - CD1 ANGL. DEV. = 12.6 DEGREES REMARK 500 ARG A 570 NE - CZ - NH2 ANGL. DEV. = -3.0 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 SER A 71 -167.46 -100.32 REMARK 500 LEU A 80 -164.96 -106.30 REMARK 500 ASN A 127 43.64 37.21 REMARK 500 HIS A 359 -69.45 66.54 REMARK 500 VAL A 383 -61.65 -132.00 REMARK 500 VAL A 410 -61.65 -100.97 REMARK 500 GLU A 419 128.59 -39.63 REMARK 500 ALA A 448 -117.07 -110.29 REMARK 500 THR A 506 -151.55 -115.13 REMARK 500 GLU A 519 -2.90 72.84 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 601 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 408 SG REMARK 620 2 CYS A 411 SG 106.8 REMARK 620 3 CYS A 426 SG 107.6 93.0 REMARK 620 4 CYS A 432 SG 120.2 108.5 116.8 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 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 0XS A 603 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3BAA RELATED DB: PDB REMARK 900 STRUCTURAL BASIS FOR THE INHIBITION OF BACTERIAL NAD+ DEPENDENT DNA REMARK 900 LIGASE REMARK 900 RELATED ID: 4GLW RELATED DB: PDB DBREF 4GLX A 1 586 UNP P15042 DNLJ_ECOLI 1 586 DBREF 4GLX B 1 26 PDB 4GLX 4GLX 1 26 DBREF 4GLX C 27 39 PDB 4GLX 4GLX 27 39 DBREF 4GLX D 40 52 PDB 4GLX 4GLX 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 DC DC SEQRES 1 D 13 DC DA DC DT DA DT DC DG DG DA DA DT DG SEQRES 1 A 586 MET GLU SER ILE GLU GLN GLN LEU THR GLU LEU ARG THR SEQRES 2 A 586 THR LEU ARG HIS HIS GLU TYR LEU TYR HIS VAL MET ASP SEQRES 3 A 586 ALA PRO GLU ILE PRO ASP ALA GLU TYR ASP ARG LEU MET SEQRES 4 A 586 ARG GLU LEU ARG GLU LEU GLU THR LYS HIS PRO GLU LEU SEQRES 5 A 586 ILE THR PRO ASP SER PRO THR GLN ARG VAL GLY ALA ALA SEQRES 6 A 586 PRO LEU ALA ALA PHE SER GLN ILE ARG HIS GLU VAL PRO SEQRES 7 A 586 MET LEU SER LEU ASP ASN VAL PHE ASP GLU GLU SER PHE SEQRES 8 A 586 LEU ALA PHE ASN LYS ARG VAL GLN ASP ARG LEU LYS ASN SEQRES 9 A 586 ASN GLU LYS VAL THR TRP CYS CYS GLU LEU LYS LEU ASP SEQRES 10 A 586 GLY LEU ALA VAL SER ILE LEU TYR GLU ASN GLY VAL LEU SEQRES 11 A 586 VAL SER ALA ALA THR ARG GLY ASP GLY THR THR GLY GLU SEQRES 12 A 586 ASP ILE THR SER ASN VAL ARG THR ILE ARG ALA ILE PRO SEQRES 13 A 586 LEU LYS LEU HIS GLY GLU ASN ILE PRO ALA ARG LEU GLU SEQRES 14 A 586 VAL ARG GLY GLU VAL PHE LEU PRO GLN ALA GLY PHE GLU SEQRES 15 A 586 LYS ILE ASN GLU ASP ALA ARG ARG THR GLY GLY LYS VAL SEQRES 16 A 586 PHE ALA ASN PRO ARG ASN ALA ALA ALA GLY SER LEU ARG SEQRES 17 A 586 GLN LEU ASP PRO ARG ILE THR ALA LYS ARG PRO LEU THR SEQRES 18 A 586 PHE PHE CYS TYR GLY VAL GLY VAL LEU GLU GLY GLY GLU SEQRES 19 A 586 LEU PRO ASP THR HIS LEU GLY ARG LEU LEU GLN PHE LYS SEQRES 20 A 586 LYS TRP GLY LEU PRO VAL SER ASP ARG VAL THR LEU CYS SEQRES 21 A 586 GLU SER ALA GLU GLU VAL LEU ALA PHE TYR HIS LYS VAL SEQRES 22 A 586 GLU GLU ASP ARG PRO THR LEU GLY PHE ASP ILE ASP GLY SEQRES 23 A 586 VAL VAL ILE LYS VAL ASN SER LEU ALA GLN GLN GLU GLN SEQRES 24 A 586 LEU GLY PHE VAL ALA ARG ALA PRO ARG TRP ALA VAL ALA SEQRES 25 A 586 PHE LYS PHE PRO ALA GLN GLU GLN MET THR PHE VAL ARG SEQRES 26 A 586 ASP VAL GLU PHE GLN VAL GLY ARG THR GLY ALA ILE THR SEQRES 27 A 586 PRO VAL ALA ARG LEU GLU PRO VAL HIS VAL ALA GLY VAL SEQRES 28 A 586 LEU VAL SER ASN ALA THR LEU HIS ASN ALA ASP GLU ILE SEQRES 29 A 586 GLU ARG LEU GLY LEU ARG ILE GLY ASP LYS VAL VAL ILE SEQRES 30 A 586 ARG ARG ALA GLY ASP VAL ILE PRO GLN VAL VAL ASN VAL SEQRES 31 A 586 VAL LEU SER GLU ARG PRO GLU ASP THR ARG GLU VAL VAL SEQRES 32 A 586 PHE PRO THR HIS CYS PRO VAL CYS GLY SER ASP VAL GLU SEQRES 33 A 586 ARG VAL GLU GLY GLU ALA VAL ALA ARG CYS THR GLY GLY SEQRES 34 A 586 LEU ILE CYS GLY ALA GLN ARG LYS GLU SER LEU LYS HIS SEQRES 35 A 586 PHE VAL SER ARG ARG ALA MET ASP VAL ASP GLY MET GLY SEQRES 36 A 586 ASP LYS ILE ILE ASP GLN LEU VAL GLU LYS GLU TYR VAL SEQRES 37 A 586 HIS THR PRO ALA ASP LEU PHE LYS LEU THR ALA GLY LYS SEQRES 38 A 586 LEU THR GLY LEU GLU ARG MET GLY PRO LYS SER ALA GLN SEQRES 39 A 586 ASN VAL VAL ASN ALA LEU GLU LYS ALA LYS GLU THR THR SEQRES 40 A 586 PHE ALA ARG PHE LEU TYR ALA LEU GLY ILE ARG GLU VAL SEQRES 41 A 586 GLY GLU ALA THR ALA ALA GLY LEU ALA ALA TYR PHE GLY SEQRES 42 A 586 THR LEU GLU ALA LEU GLU ALA ALA SER ILE GLU GLU LEU SEQRES 43 A 586 GLN LYS VAL PRO ASP VAL GLY ILE VAL VAL ALA SER HIS SEQRES 44 A 586 VAL HIS ASN PHE PHE ALA GLU GLU SER ASN ARG ASN VAL SEQRES 45 A 586 ILE SER GLU LEU LEU ALA GLU GLY VAL HIS TRP PRO ALA SEQRES 46 A 586 PRO HET ZN A 601 1 HET SO4 A 602 5 HET 0XS A 603 19 HETNAM ZN ZINC ION HETNAM SO4 SULFATE ION HETNAM 0XS 2-AMINO-6-BROMO-7-(TRIFLUOROMETHYL)-1,8-NAPHTHYRIDINE- HETNAM 2 0XS 3-CARBOXAMIDE FORMUL 5 ZN ZN 2+ FORMUL 6 SO4 O4 S 2- FORMUL 7 0XS C10 H6 BR F3 N4 O FORMUL 8 HOH *204(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 PRO A 50 ILE A 53 5 4 HELIX 4 4 SER A 57 ARG A 61 5 5 HELIX 5 5 ASP A 87 ARG A 101 1 15 HELIX 6 6 ILE A 145 ARG A 150 1 6 HELIX 7 7 PRO A 177 THR A 191 1 15 HELIX 8 8 ASN A 198 ARG A 208 1 11 HELIX 9 9 ASP A 211 LYS A 217 1 7 HELIX 10 10 THR A 238 TRP A 249 1 12 HELIX 11 11 SER A 262 ARG A 277 1 16 HELIX 12 12 PRO A 278 LEU A 280 5 3 HELIX 13 13 SER A 293 GLY A 301 1 9 HELIX 14 14 ASN A 360 GLY A 368 1 9 HELIX 15 15 GLY A 381 VAL A 383 5 3 HELIX 16 16 LEU A 392 ARG A 395 5 4 HELIX 17 17 GLY A 428 ILE A 431 5 4 HELIX 18 18 CYS A 432 SER A 445 1 14 HELIX 19 19 GLY A 455 LYS A 465 1 11 HELIX 20 20 THR A 470 LYS A 476 5 7 HELIX 21 21 THR A 478 GLY A 484 1 7 HELIX 22 22 GLY A 489 LYS A 504 1 16 HELIX 23 23 THR A 507 LEU A 515 1 9 HELIX 24 24 GLY A 521 GLY A 533 1 13 HELIX 25 25 THR A 534 ALA A 541 1 8 HELIX 26 26 SER A 542 GLN A 547 1 6 HELIX 27 27 GLY A 553 GLU A 566 1 14 HELIX 28 28 GLU A 566 GLU A 579 1 14 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 ASN A 84 VAL A 85 0 SHEET 2 B 5 ALA A 310 PHE A 313 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 GLU A 113 O VAL A 288 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 THR A 135 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 TYR A 225 N ARG A 171 SHEET 1 D 5 VAL A 351 THR A 357 0 SHEET 2 D 5 ILE A 337 VAL A 348 -1 N VAL A 346 O VAL A 353 SHEET 3 D 5 GLU A 319 VAL A 331 -1 N GLN A 330 O THR A 338 SHEET 4 D 5 LYS A 374 ALA A 380 -1 O VAL A 375 N THR A 322 SHEET 5 D 5 ILE A 384 VAL A 390 -1 O ILE A 384 N ALA A 380 SHEET 1 E 2 ARG A 370 ILE A 371 0 SHEET 2 E 2 ARG A 400 GLU A 401 -1 O ARG A 400 N ILE A 371 SHEET 1 F 2 VAL A 415 GLU A 416 0 SHEET 2 F 2 ARG A 425 CYS A 426 -1 O ARG A 425 N GLU A 416 LINK SG CYS A 408 ZN ZN A 601 1555 1555 2.25 LINK SG CYS A 411 ZN ZN A 601 1555 1555 2.34 LINK SG CYS A 426 ZN ZN A 601 1555 1555 2.28 LINK SG CYS A 432 ZN ZN A 601 1555 1555 2.33 SITE 1 AC1 4 CYS A 408 CYS A 411 CYS A 426 CYS A 432 SITE 1 AC2 3 ARG A 74 ARG A 510 HOH A 850 SITE 1 AC3 13 LEU A 80 GLU A 113 LEU A 114 LYS A 115 SITE 2 AC3 13 LEU A 116 GLU A 173 TYR A 225 VAL A 288 SITE 3 AC3 13 LYS A 290 PRO A 307 TRP A 309 HOH A 788 SITE 4 AC3 13 HOH A 849 CRYST1 110.990 100.140 86.570 90.00 105.50 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 0.009010 0.000000 0.002499 0.00000 SCALE2 0.000000 0.009986 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011987 0.00000