HEADER LIGASE/LIGASE INHIBITOR 15-AUG-12 4GLW TITLE DNA LIGASE A IN COMPLEX WITH INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA LIGASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: POLYDEOXYRIBONUCLEOTIDE SYNTHASE [NAD(+)]; COMPND 5 EC: 6.5.1.2; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOCOCCUS PNEUMONIAE; SOURCE 3 ORGANISM_TAXID: 488223; SOURCE 4 STRAIN: P1031; SOURCE 5 GENE: LIGA, SPP_1122; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS DNA LIGASE A, INHIBITOR, LIGASE-LIGASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR L.PRADE,R.LANGE,N.TIDTEN-LUKSCH,A.CHAMBOVEY REVDAT 4 28-FEB-24 4GLW 1 REMARK REVDAT 3 15-NOV-17 4GLW 1 REMARK REVDAT 2 31-OCT-12 4GLW 1 JRNL REVDAT 1 10-OCT-12 4GLW 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. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.41 REMARK 3 DATA CUTOFF (SIGMA(F)) : 3.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 48105 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) : 0.209 REMARK 3 R VALUE (WORKING SET) : 0.207 REMARK 3 FREE R VALUE : 0.260 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 2203 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) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 REFLECTION IN BIN (WORKING SET) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE SET COUNT : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4206 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 62 REMARK 3 SOLVENT ATOMS : 110 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 40.14 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 38.47 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL 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): NULL REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : NULL REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): NULL ; NULL ; NULL REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): NULL ; NULL ; NULL REMARK 3 GENERAL PLANES REFINED ATOMS (A): NULL ; NULL ; NULL 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 : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : NULL REMARK 3 ION PROBE RADIUS : NULL REMARK 3 SHRINKAGE RADIUS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4GLW 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_1000074347. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-NOV-07 REMARK 200 TEMPERATURE (KELVIN) : 113 REMARK 200 PH : 7 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 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 : 48105 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 39.410 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.11900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.5100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.20 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.43000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.370 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 (%): 53.72 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.66 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.6 M SODIUM FORMIATE, 0.1 M HEPES, 36 REMARK 280 % (W/V) PEG 4000, PH 7, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 65.97667 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 131.95333 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1880 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 26360 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -38.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 MET A 1 REMARK 465 LEU A 8 REMARK 465 VAL A 9 REMARK 465 ALA A 10 REMARK 465 LEU A 11 REMARK 465 LEU A 12 REMARK 465 ASN A 13 REMARK 465 ARG A 14 REMARK 465 TYR A 15 REMARK 465 ALA A 16 REMARK 465 THR A 17 REMARK 465 GLU A 18 REMARK 465 TYR A 19 REMARK 465 TYR A 20 REMARK 465 THR A 21 REMARK 465 SER A 22 REMARK 465 ASP A 23 REMARK 465 ASN A 24 REMARK 465 PRO A 25 REMARK 465 SER A 26 REMARK 465 VAL A 27 REMARK 465 SER A 28 REMARK 465 ASP A 29 REMARK 465 SER A 30 REMARK 465 GLU A 31 REMARK 465 TYR A 32 REMARK 465 ASP A 33 REMARK 465 ARG A 34 REMARK 465 LEU A 35 REMARK 465 TYR A 36 REMARK 465 MET B 1 REMARK 465 ARG B 14 REMARK 465 TYR B 15 REMARK 465 ALA B 16 REMARK 465 THR B 17 REMARK 465 GLU B 18 REMARK 465 TYR B 19 REMARK 465 TYR B 20 REMARK 465 THR B 21 REMARK 465 SER B 22 REMARK 465 ASP B 23 REMARK 465 ASN B 24 REMARK 465 PRO B 25 REMARK 465 SER B 26 REMARK 465 VAL B 27 REMARK 465 SER B 28 REMARK 465 ASP B 29 REMARK 465 SER B 30 REMARK 465 GLU B 31 REMARK 465 TYR B 32 REMARK 465 ASP B 33 REMARK 465 ARG B 34 REMARK 465 LEU B 35 REMARK 465 ALA B 305 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 ASN A 2 CG OD1 ND2 REMARK 470 LYS A 3 CG CD CE NZ REMARK 470 ARG A 4 CG CD NE CZ NH1 NH2 REMARK 470 ASN A 6 CG OD1 ND2 REMARK 470 GLU A 7 CG CD OE1 OE2 REMARK 470 ARG A 37 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 38 CG CD OE1 OE2 REMARK 470 LEU A 39 CG CD1 CD2 REMARK 470 VAL A 40 CG1 CG2 REMARK 470 GLU A 41 CG CD OE1 OE2 REMARK 470 LEU A 42 CG CD1 CD2 REMARK 470 GLU A 43 CG CD OE1 OE2 REMARK 470 TYR A 46 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 GLU A 48 CG CD OE1 OE2 REMARK 470 GLN A 49 CG CD OE1 NE2 REMARK 470 VAL A 50 CG1 CG2 REMARK 470 ASP A 53 CG OD1 OD2 REMARK 470 LEU A 64 CG CD1 CD2 REMARK 470 ASP A 65 CG OD1 OD2 REMARK 470 GLU A 68 CG CD OE1 OE2 REMARK 470 LYS A 69 CG CD CE NZ REMARK 470 GLU A 86 CG CD OE1 OE2 REMARK 470 GLU A 98 CG CD OE1 OE2 REMARK 470 ILE A 135 CG1 CG2 CD1 REMARK 470 LYS A 147 CG CD CE NZ REMARK 470 ASP A 173 CG OD1 OD2 REMARK 470 GLN A 177 CG CD OE1 NE2 REMARK 470 LYS A 244 CG CD CE NZ REMARK 470 GLU A 249 CG CD OE1 OE2 REMARK 470 ILE A 251 CG1 CG2 CD1 REMARK 470 GLU A 266 CG CD OE1 OE2 REMARK 470 LYS A 293 CG CD CE NZ REMARK 470 ASN B 2 CG OD1 ND2 REMARK 470 LYS B 3 CG CD CE NZ REMARK 470 ARG B 4 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 7 CG CD OE1 OE2 REMARK 470 LEU B 8 CG CD1 CD2 REMARK 470 VAL B 9 CG1 CG2 REMARK 470 LEU B 11 CG CD1 CD2 REMARK 470 LEU B 12 CG CD1 CD2 REMARK 470 ASN B 13 CG OD1 ND2 REMARK 470 TYR B 36 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 ARG B 37 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 38 CG CD OE1 OE2 REMARK 470 VAL B 40 CG1 CG2 REMARK 470 GLU B 41 CG CD OE1 OE2 REMARK 470 THR B 44 OG1 CG2 REMARK 470 GLU B 48 CG CD OE1 OE2 REMARK 470 GLN B 49 CG CD OE1 NE2 REMARK 470 VAL B 50 CG1 CG2 REMARK 470 LEU B 51 CG CD1 CD2 REMARK 470 LYS B 147 CG CD CE NZ REMARK 470 GLU B 181 CG CD OE1 OE2 REMARK 470 ARG B 199 CG CD NE CZ NH1 NH2 REMARK 470 ILE B 251 CG1 CG2 CD1 REMARK 470 GLN B 263 CG CD OE1 NE2 REMARK 470 GLU B 264 CG CD OE1 OE2 REMARK 470 GLU B 266 CG CD OE1 OE2 REMARK 470 VAL B 292 CG1 CG2 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 ARG A 96 NE - CZ - NH1 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG A 145 CG - CD - NE ANGL. DEV. = -18.6 DEGREES REMARK 500 ARG A 145 CD - NE - CZ ANGL. DEV. = 9.6 DEGREES REMARK 500 ARG A 145 NE - CZ - NH1 ANGL. DEV. = 5.2 DEGREES REMARK 500 ARG A 145 NE - CZ - NH2 ANGL. DEV. = -8.7 DEGREES REMARK 500 ASP A 148 CB - CA - C ANGL. DEV. = -13.4 DEGREES REMARK 500 ARG A 209 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 ARG A 209 NE - CZ - NH2 ANGL. DEV. = -4.0 DEGREES REMARK 500 LEU A 215 CA - CB - CG ANGL. DEV. = -16.0 DEGREES REMARK 500 ASP A 225 CB - CG - OD1 ANGL. DEV. = -5.4 DEGREES REMARK 500 ARG B 58 NE - CZ - NH1 ANGL. DEV. = -3.7 DEGREES REMARK 500 ARG B 58 NE - CZ - NH2 ANGL. DEV. = 3.7 DEGREES REMARK 500 ARG B 145 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 ASP B 148 CB - CA - C ANGL. DEV. = -13.1 DEGREES REMARK 500 ASP B 148 CB - CG - OD2 ANGL. DEV. = -7.4 DEGREES REMARK 500 ASP B 202 CB - CG - OD1 ANGL. DEV. = 6.3 DEGREES REMARK 500 LEU B 215 CA - CB - CG ANGL. DEV. = -20.5 DEGREES REMARK 500 ARG B 245 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 ARG B 245 NE - CZ - NH2 ANGL. DEV. = -3.2 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 ARG A 4 -75.21 -48.71 REMARK 500 TYR A 46 62.71 -112.76 REMARK 500 GLU A 48 -4.66 -52.34 REMARK 500 GLN A 49 46.66 -149.56 REMARK 500 ASP A 65 -77.22 -67.92 REMARK 500 LEU B 11 -80.54 -55.45 REMARK 500 LEU B 12 -31.41 -34.63 REMARK 500 TYR B 46 73.37 -119.63 REMARK 500 GLU B 48 42.99 -78.82 REMARK 500 GLN B 49 19.57 -153.18 REMARK 500 SER B 78 -169.12 -110.94 REMARK 500 ILE B 251 -17.94 -44.20 REMARK 500 THR B 291 -161.89 -75.41 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 0XT A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 0XT B 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NMN B 403 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: 4GLX RELATED DB: PDB DBREF 4GLW A 1 305 UNP C1CKI0 DNLJ_STRZP 1 305 DBREF 4GLW B 1 305 UNP C1CKI0 DNLJ_STRZP 1 305 SEQRES 1 A 305 MET ASN LYS ARG MET ASN GLU LEU VAL ALA LEU LEU ASN SEQRES 2 A 305 ARG TYR ALA THR GLU TYR TYR THR SER ASP ASN PRO SER SEQRES 3 A 305 VAL SER ASP SER GLU TYR ASP ARG LEU TYR ARG GLU LEU SEQRES 4 A 305 VAL GLU LEU GLU THR ALA TYR PRO GLU GLN VAL LEU ALA SEQRES 5 A 305 ASP SER PRO THR HIS ARG VAL GLY GLY LYS VAL LEU ASP SEQRES 6 A 305 GLY PHE GLU LYS TYR SER HIS GLN TYR PRO LEU TYR SER SEQRES 7 A 305 LEU GLN ASP ALA PHE SER ARG GLU GLU LEU ASP ALA PHE SEQRES 8 A 305 ASP ALA ARG VAL ARG LYS GLU VAL ALA HIS PRO THR TYR SEQRES 9 A 305 ILE CYS GLU LEU LYS ILE ASP GLY LEU SER ILE SER LEU SEQRES 10 A 305 THR TYR GLU LYS GLY ILE LEU VAL ALA GLY VAL THR ARG SEQRES 11 A 305 GLY ASP GLY SER ILE GLY GLU ASN ILE THR GLU ASN LEU SEQRES 12 A 305 LYS ARG VAL LYS ASP ILE PRO LEU THR LEU PRO GLU GLU SEQRES 13 A 305 LEU ASP ILE THR VAL ARG GLY GLU CYS TYR MET PRO ARG SEQRES 14 A 305 ALA SER PHE ASP GLN VAL ASN GLN ALA ARG GLN GLU ASN SEQRES 15 A 305 GLY GLU PRO GLU PHE ALA ASN PRO ARG ASN ALA ALA ALA SEQRES 16 A 305 GLY THR LEU ARG GLN LEU ASP THR ALA VAL VAL ALA LYS SEQRES 17 A 305 ARG ASN LEU ALA THR PHE LEU TYR GLN GLU ALA SER PRO SEQRES 18 A 305 SER THR ARG ASP SER GLN GLU LYS GLY LEU LYS TYR LEU SEQRES 19 A 305 GLU GLN LEU GLY PHE VAL VAL ASN PRO LYS ARG ILE LEU SEQRES 20 A 305 ALA GLU ASN ILE ASP GLU ILE TRP ASN PHE ILE GLN GLU SEQRES 21 A 305 VAL GLY GLN GLU ARG GLU ASN LEU PRO TYR ASP ILE ASP SEQRES 22 A 305 GLY VAL VAL ILE LYS VAL ASN ASP LEU ALA SER GLN GLU SEQRES 23 A 305 GLU LEU GLY PHE THR VAL LYS ALA PRO LYS TRP ALA VAL SEQRES 24 A 305 ALA TYR LYS PHE PRO ALA SEQRES 1 B 305 MET ASN LYS ARG MET ASN GLU LEU VAL ALA LEU LEU ASN SEQRES 2 B 305 ARG TYR ALA THR GLU TYR TYR THR SER ASP ASN PRO SER SEQRES 3 B 305 VAL SER ASP SER GLU TYR ASP ARG LEU TYR ARG GLU LEU SEQRES 4 B 305 VAL GLU LEU GLU THR ALA TYR PRO GLU GLN VAL LEU ALA SEQRES 5 B 305 ASP SER PRO THR HIS ARG VAL GLY GLY LYS VAL LEU ASP SEQRES 6 B 305 GLY PHE GLU LYS TYR SER HIS GLN TYR PRO LEU TYR SER SEQRES 7 B 305 LEU GLN ASP ALA PHE SER ARG GLU GLU LEU ASP ALA PHE SEQRES 8 B 305 ASP ALA ARG VAL ARG LYS GLU VAL ALA HIS PRO THR TYR SEQRES 9 B 305 ILE CYS GLU LEU LYS ILE ASP GLY LEU SER ILE SER LEU SEQRES 10 B 305 THR TYR GLU LYS GLY ILE LEU VAL ALA GLY VAL THR ARG SEQRES 11 B 305 GLY ASP GLY SER ILE GLY GLU ASN ILE THR GLU ASN LEU SEQRES 12 B 305 LYS ARG VAL LYS ASP ILE PRO LEU THR LEU PRO GLU GLU SEQRES 13 B 305 LEU ASP ILE THR VAL ARG GLY GLU CYS TYR MET PRO ARG SEQRES 14 B 305 ALA SER PHE ASP GLN VAL ASN GLN ALA ARG GLN GLU ASN SEQRES 15 B 305 GLY GLU PRO GLU PHE ALA ASN PRO ARG ASN ALA ALA ALA SEQRES 16 B 305 GLY THR LEU ARG GLN LEU ASP THR ALA VAL VAL ALA LYS SEQRES 17 B 305 ARG ASN LEU ALA THR PHE LEU TYR GLN GLU ALA SER PRO SEQRES 18 B 305 SER THR ARG ASP SER GLN GLU LYS GLY LEU LYS TYR LEU SEQRES 19 B 305 GLU GLN LEU GLY PHE VAL VAL ASN PRO LYS ARG ILE LEU SEQRES 20 B 305 ALA GLU ASN ILE ASP GLU ILE TRP ASN PHE ILE GLN GLU SEQRES 21 B 305 VAL GLY GLN GLU ARG GLU ASN LEU PRO TYR ASP ILE ASP SEQRES 22 B 305 GLY VAL VAL ILE LYS VAL ASN ASP LEU ALA SER GLN GLU SEQRES 23 B 305 GLU LEU GLY PHE THR VAL LYS ALA PRO LYS TRP ALA VAL SEQRES 24 B 305 ALA TYR LYS PHE PRO ALA HET SO4 A 401 5 HET 0XT A 402 15 HET SO4 B 401 5 HET 0XT B 402 15 HET NMN B 403 22 HETNAM SO4 SULFATE ION HETNAM 0XT 7-METHOXY-6-METHYLPTERIDINE-2,4-DIAMINE HETNAM NMN BETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE HETSYN NMN NICOTINAMIDE MONONUCLEOTIDE FORMUL 3 SO4 2(O4 S 2-) FORMUL 4 0XT 2(C8 H10 N6 O) FORMUL 7 NMN C11 H16 N2 O8 P 1+ FORMUL 8 HOH *110(H2 O) HELIX 1 1 ASN A 2 GLU A 7 1 6 HELIX 2 2 GLU A 38 TYR A 46 1 9 HELIX 3 3 PRO A 47 VAL A 50 5 4 HELIX 4 4 SER A 54 VAL A 59 5 6 HELIX 5 5 SER A 84 ARG A 96 1 13 HELIX 6 6 ILE A 139 LYS A 144 1 6 HELIX 7 7 PRO A 168 ASN A 182 1 15 HELIX 8 8 ASN A 189 ARG A 199 1 11 HELIX 9 9 ASP A 202 ARG A 209 1 8 HELIX 10 10 SER A 226 GLY A 238 1 13 HELIX 11 11 ASN A 250 ARG A 265 1 16 HELIX 12 12 GLU A 266 LEU A 268 5 3 HELIX 13 13 ASP A 281 GLY A 289 1 9 HELIX 14 14 LYS B 3 ASN B 13 1 11 HELIX 15 15 ARG B 37 TYR B 46 1 10 HELIX 16 16 PRO B 47 VAL B 50 5 4 HELIX 17 17 SER B 54 VAL B 59 5 6 HELIX 18 18 SER B 84 LYS B 97 1 14 HELIX 19 19 ILE B 139 LYS B 144 1 6 HELIX 20 20 PRO B 168 ASN B 182 1 15 HELIX 21 21 ASN B 189 GLN B 200 1 12 HELIX 22 22 ASP B 202 ARG B 209 1 8 HELIX 23 23 SER B 226 LEU B 237 1 12 HELIX 24 24 ASN B 250 ARG B 265 1 16 HELIX 25 25 GLU B 266 LEU B 268 5 3 HELIX 26 26 ASP B 281 GLY B 289 1 9 SHEET 1 A 2 GLU A 68 SER A 71 0 SHEET 2 A 2 ILE A 135 ASN A 138 -1 O ASN A 138 N GLU A 68 SHEET 1 B 5 ASP A 81 ALA A 82 0 SHEET 2 B 5 ALA A 298 LYS A 302 1 O LYS A 302 N ALA A 82 SHEET 3 B 5 ILE A 272 VAL A 279 -1 N VAL A 275 O TYR A 301 SHEET 4 B 5 TYR A 104 ILE A 110 -1 N ILE A 105 O LYS A 278 SHEET 5 B 5 ILE A 246 ALA A 248 -1 O ALA A 248 N TYR A 104 SHEET 1 C 4 ILE A 123 THR A 129 0 SHEET 2 C 4 LEU A 113 GLU A 120 -1 N THR A 118 O VAL A 125 SHEET 3 C 4 ILE A 159 TYR A 166 -1 O CYS A 165 N LEU A 113 SHEET 4 C 4 ALA A 212 GLU A 218 -1 O GLN A 217 N ARG A 162 SHEET 1 D 2 LYS B 69 SER B 71 0 SHEET 2 D 2 ILE B 135 GLU B 137 -1 O GLY B 136 N TYR B 70 SHEET 1 E 5 ASP B 81 ALA B 82 0 SHEET 2 E 5 ALA B 298 TYR B 301 1 O ALA B 300 N ALA B 82 SHEET 3 E 5 ILE B 272 VAL B 279 -1 N ILE B 277 O VAL B 299 SHEET 4 E 5 TYR B 104 ILE B 110 -1 N LYS B 109 O ASP B 273 SHEET 5 E 5 ILE B 246 ALA B 248 -1 O ALA B 248 N TYR B 104 SHEET 1 F 4 ILE B 123 THR B 129 0 SHEET 2 F 4 LEU B 113 GLU B 120 -1 N SER B 116 O VAL B 128 SHEET 3 F 4 ILE B 159 TYR B 166 -1 O ILE B 159 N TYR B 119 SHEET 4 F 4 ALA B 212 GLU B 218 -1 O GLN B 217 N ARG B 162 SITE 1 AC1 5 ARG A 224 ASP A 225 LYS A 229 LEU B 157 SITE 2 AC1 5 ASP B 158 SITE 1 AC2 10 TYR A 77 LEU A 79 GLU A 107 LEU A 108 SITE 2 AC2 10 TYR A 216 GLN A 217 VAL A 276 LYS A 278 SITE 3 AC2 10 TRP A 297 HOH A 505 SITE 1 AC3 6 LEU A 157 ASP A 158 ARG B 224 ASP B 225 SITE 2 AC3 6 LYS B 229 HOH B 505 SITE 1 AC4 10 TYR B 77 LEU B 79 GLU B 107 LEU B 108 SITE 2 AC4 10 LYS B 109 GLU B 164 TYR B 216 LYS B 278 SITE 3 AC4 10 TRP B 297 HOH B 510 SITE 1 AC5 8 ASP B 53 LYS B 121 GLY B 122 THR B 152 SITE 2 AC5 8 LEU B 153 PRO B 154 GLU B 155 GLU B 156 CRYST1 56.730 56.730 197.930 90.00 90.00 120.00 P 31 6 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.017627 0.010177 0.000000 0.00000 SCALE2 0.000000 0.020354 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005052 0.00000