HEADER ISOMERASE 30-JUN-14 4URL TITLE CRYSTAL STRUCTURE OF STAPH PARE43KDA IN COMPLEX WITH KBD COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA TOPOISOMERASE IV, B SUBUNIT; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: 43KDA N-TERMINAL DOMAIN, RESIDUES 1-406; COMPND 5 SYNONYM: TOPOISOMERASE IV PARE; COMPND 6 EC: 5.99.1.-; COMPND 7 ENGINEERED: YES; COMPND 8 OTHER_DETAILS: KIBDELOMYCIN SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AUREUS; SOURCE 3 ORGANISM_TAXID: 1280; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_VECTOR: PGEX-4T3 KEYWDS ISOMERASE, ANTIBIOTICS, NATURAL PRODUCT, KIBDELOMYCIN, GYRASE, KEYWDS 2 TOPOISOMERASE IV EXPDTA X-RAY DIFFRACTION AUTHOR J.LU,S.PATEL,N.SHARMA,S.SOISSON,R.KISHII,M.TAKEI,Y.FUKUDA,K.J.LUMB, AUTHOR 2 S.B.SINGH REVDAT 3 10-JAN-24 4URL 1 REMARK REVDAT 2 01-OCT-14 4URL 1 JRNL REVDAT 1 16-JUL-14 4URL 0 JRNL AUTH J.LU,S.PATEL,N.SHARMA,S.M.SOISSON,R.KISHII,M.TAKEI,Y.FUKUDA, JRNL AUTH 2 K.J.LUMB,S.B.SINGH JRNL TITL STRUCTURES OF KIBDELOMYCIN BOUND TO STAPHYLOCOCCUS AUREUS JRNL TITL 2 GYRB AND PARE SHOWED A NOVEL U-SHAPED BINDING MODE. JRNL REF ACS CHEM.BIOL. V. 9 2023 2014 JRNL REFN ISSN 1554-8929 JRNL PMID 24992706 JRNL DOI 10.1021/CB5001197 REMARK 2 REMARK 2 RESOLUTION. 2.29 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.11.5 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.29 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.73 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 41708 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) : 0.218 REMARK 3 R VALUE (WORKING SET) : 0.217 REMARK 3 FREE R VALUE : 0.252 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.140 REMARK 3 FREE R VALUE TEST SET COUNT : 1311 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 : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 2.29 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 2.35 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.81 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 2666 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2484 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2586 REMARK 3 BIN R VALUE (WORKING SET) : 0.2482 REMARK 3 BIN FREE R VALUE : 0.2532 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 3.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 80 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 : 5507 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 128 REMARK 3 SOLVENT ATOMS : 106 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 52.27 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 53.93 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -5.54740 REMARK 3 B22 (A**2) : 3.17370 REMARK 3 B33 (A**2) : 2.37370 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -13.58690 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.348 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.260 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.207 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.276 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.215 REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.924 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.900 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 5736 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 7774 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 2039 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 150 ; 8.000 ; HARMONIC REMARK 3 GENERAL PLANES : 878 ; 8.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 5736 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : NULL ; NULL ; NULL REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 769 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 6543 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.21 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 2.18 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 19.76 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4URL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 30-JUN-14. REMARK 100 THE DEPOSITION ID IS D_1290061134. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-FEB-09 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 17-ID 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 : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 41758 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.700 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL 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) : 2.34 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.00 REMARK 200 R MERGE FOR SHELL (I) : 0.57000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 20.30 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: PDB ENTRY 1S16 REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.71 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.66 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M AMMONIUM SULFATE, 0.1M TRIS PH REMARK 280 8.5 AND 25% PEG 3350 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 68.40450 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 ALA A 2 REMARK 465 MET A 3 REMARK 465 ASN A 4 REMARK 465 LYS A 5 REMARK 465 GLN A 6 REMARK 465 ASN A 7 REMARK 465 ASN A 8 REMARK 465 TYR A 9 REMARK 465 SER A 10 REMARK 465 ASP A 11 REMARK 465 ASP A 12 REMARK 465 SER A 13 REMARK 465 ILE A 14 REMARK 465 GLN A 15 REMARK 465 VAL A 16 REMARK 465 LEU A 17 REMARK 465 GLY A 104 REMARK 465 LYS A 105 REMARK 465 PHE A 106 REMARK 465 GLY A 107 REMARK 465 GLN A 108 REMARK 465 GLY A 109 REMARK 465 GLY A 110 REMARK 465 TYR A 111 REMARK 465 LYS A 112 REMARK 465 THR A 113 REMARK 465 SER A 114 REMARK 465 GLY A 115 REMARK 465 GLY A 116 REMARK 465 LEU A 117 REMARK 465 LYS A 310 REMARK 465 GLU A 339 REMARK 465 GLY A 340 REMARK 465 GLN A 341 REMARK 465 THR A 342 REMARK 465 GLY A 401 REMARK 465 LYS A 402 REMARK 465 LYS A 403 REMARK 465 ASN A 404 REMARK 465 LYS A 405 REMARK 465 ARG A 406 REMARK 465 MET B 1 REMARK 465 ALA B 2 REMARK 465 MET B 3 REMARK 465 ASN B 4 REMARK 465 LYS B 5 REMARK 465 GLN B 6 REMARK 465 ASN B 7 REMARK 465 ASN B 8 REMARK 465 TYR B 9 REMARK 465 SER B 10 REMARK 465 ASP B 11 REMARK 465 ASP B 12 REMARK 465 SER B 13 REMARK 465 ILE B 14 REMARK 465 GLN B 15 REMARK 465 VAL B 16 REMARK 465 LEU B 17 REMARK 465 GLU B 18 REMARK 465 GLY B 19 REMARK 465 LYS B 105 REMARK 465 PHE B 106 REMARK 465 GLY B 107 REMARK 465 GLN B 108 REMARK 465 GLY B 109 REMARK 465 GLY B 110 REMARK 465 TYR B 111 REMARK 465 LYS B 112 REMARK 465 THR B 113 REMARK 465 SER B 114 REMARK 465 GLY B 115 REMARK 465 GLY B 116 REMARK 465 LEU B 117 REMARK 465 HIS B 118 REMARK 465 GLU B 339 REMARK 465 GLY B 340 REMARK 465 GLN B 341 REMARK 465 SER B 400 REMARK 465 GLY B 401 REMARK 465 LYS B 402 REMARK 465 LYS B 403 REMARK 465 ASN B 404 REMARK 465 LYS B 405 REMARK 465 ARG B 406 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 GLU A 18 CG CD OE1 OE2 REMARK 470 LYS A 25 CG CD CE NZ REMARK 470 ARG A 26 CG CD NE CZ NH1 NH2 REMARK 470 MET A 29 CG SD CE REMARK 470 LYS A 36 CG CD CE NZ REMARK 470 LYS A 90 CG CD CE NZ REMARK 470 LYS A 148 CG CD CE NZ REMARK 470 LYS A 159 CG CD CE NZ REMARK 470 LYS A 160 CG CD CE NZ REMARK 470 LYS A 162 CG CD CE NZ REMARK 470 LYS A 164 CG CD CE NZ REMARK 470 LYS A 205 CG CD CE NZ REMARK 470 HIS A 220 CG ND1 CD2 CE1 NE2 REMARK 470 GLN A 265 CG CD OE1 NE2 REMARK 470 LYS A 280 CG CD CE NZ REMARK 470 ASP A 315 CG OD1 OD2 REMARK 470 GLU A 333 CG CD OE1 OE2 REMARK 470 LEU A 335 CG CD1 CD2 REMARK 470 GLN A 337 CG CD OE1 NE2 REMARK 470 LYS A 343 CG CD CE NZ REMARK 470 LYS A 345 CG CD CE NZ REMARK 470 GLN A 372 CG CD OE1 NE2 REMARK 470 GLU A 396 CG CD OE1 OE2 REMARK 470 LEU B 20 N REMARK 470 GLU B 21 CG CD OE1 OE2 REMARK 470 LYS B 25 CG CD CE NZ REMARK 470 ARG B 26 CG CD NE CZ NH1 NH2 REMARK 470 ASP B 35 CG OD1 OD2 REMARK 470 ARG B 37 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 148 CG CD CE NZ REMARK 470 LYS B 162 CG CD CE NZ REMARK 470 LYS B 164 CG CD CE NZ REMARK 470 LYS B 180 CG CD CE NZ REMARK 470 ASN B 186 CG OD1 ND2 REMARK 470 LYS B 215 CG CD CE NZ REMARK 470 ARG B 217 CG CD NE CZ NH1 NH2 REMARK 470 HIS B 220 CG ND1 CD2 CE1 NE2 REMARK 470 GLU B 250 CG CD OE1 OE2 REMARK 470 LYS B 310 CG CD CE NZ REMARK 470 LYS B 312 CG CD CE NZ REMARK 470 GLU B 333 CG CD OE1 OE2 REMARK 470 GLN B 337 CG CD OE1 NE2 REMARK 470 GLU B 369 CG CD OE1 OE2 REMARK 470 GLN B 372 CG CD OE1 NE2 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 ASP A 35 -159.61 -102.79 REMARK 500 ASN A 60 2.84 -155.34 REMARK 500 SER A 88 -158.51 -75.02 REMARK 500 ASN A 149 -121.24 60.28 REMARK 500 SER A 182 30.74 -150.79 REMARK 500 ASN A 252 -128.61 66.19 REMARK 500 SER A 344 -15.26 58.04 REMARK 500 THR A 348 96.96 -48.07 REMARK 500 LYS A 370 58.86 -107.06 REMARK 500 ASN B 60 19.62 -157.74 REMARK 500 ASN B 149 -120.24 56.34 REMARK 500 ALA B 181 -164.20 112.07 REMARK 500 SER B 213 106.03 -46.78 REMARK 500 THR B 279 79.34 -114.91 REMARK 500 THR B 348 104.98 -45.08 REMARK 500 LYS B 370 50.20 -103.67 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 XAM A 2000 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE XAM B 2000 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4URM RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF STAPH GYRASEB 24KDA IN COMPLEX WITH REMARK 900 KIBDELOMYCIN REMARK 900 RELATED ID: 4URN RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF STAPH PARE 24KDA IN COMPLEX WITH NOVOBIOCIN REMARK 900 RELATED ID: 4URO RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF STAPH GYRASEB 24KDA IN COMPLEX WITH NOVOBIOCIN DBREF 4URL A 1 406 UNP X5EN43 X5EN43_STAAU 1 406 DBREF 4URL B 1 406 UNP X5EN43 X5EN43_STAAU 1 406 SEQRES 1 A 406 MET ALA MET ASN LYS GLN ASN ASN TYR SER ASP ASP SER SEQRES 2 A 406 ILE GLN VAL LEU GLU GLY LEU GLU ALA VAL ARG LYS ARG SEQRES 3 A 406 PRO GLY MET TYR ILE GLY SER THR ASP LYS ARG GLY LEU SEQRES 4 A 406 HIS HIS LEU VAL TYR GLU ILE VAL ASP ASN SER VAL ASP SEQRES 5 A 406 GLU VAL LEU ASN GLY TYR GLY ASN GLU ILE ASP VAL THR SEQRES 6 A 406 ILE ASN LYS ASP GLY SER ILE SER ILE GLU ASP ASN GLY SEQRES 7 A 406 ARG GLY MET PRO THR GLY ILE HIS LYS SER GLY LYS PRO SEQRES 8 A 406 THR VAL GLU VAL ILE PHE THR VAL LEU HIS ALA GLY GLY SEQRES 9 A 406 LYS PHE GLY GLN GLY GLY TYR LYS THR SER GLY GLY LEU SEQRES 10 A 406 HIS GLY VAL GLY ALA SER VAL VAL ASN ALA LEU SER GLU SEQRES 11 A 406 TRP LEU GLU VAL GLU ILE HIS ARG ASP GLY ASN ILE TYR SEQRES 12 A 406 HIS GLN SER PHE LYS ASN GLY GLY SER PRO SER SER GLY SEQRES 13 A 406 LEU VAL LYS LYS GLY LYS THR LYS LYS THR GLY THR LYS SEQRES 14 A 406 VAL THR PHE LYS PRO ASP ASP THR ILE PHE LYS ALA SER SEQRES 15 A 406 THR SER PHE ASN PHE ASP VAL LEU SER GLU ARG LEU GLN SEQRES 16 A 406 GLU SER ALA PHE LEU LEU LYS ASN LEU LYS ILE THR LEU SEQRES 17 A 406 ASN ASP LEU ARG SER GLY LYS GLU ARG GLN GLU HIS TYR SEQRES 18 A 406 HIS TYR GLU GLU GLY ILE LYS GLU PHE VAL SER TYR VAL SEQRES 19 A 406 ASN GLU GLY LYS GLU VAL LEU HIS ASP VAL ALA THR PHE SEQRES 20 A 406 SER GLY GLU ALA ASN GLY ILE GLU VAL ASP VAL ALA PHE SEQRES 21 A 406 GLN TYR ASN ASP GLN TYR SER GLU SER ILE LEU SER PHE SEQRES 22 A 406 VAL ASN ASN VAL ARG THR LYS ASP GLY GLY THR HIS GLU SEQRES 23 A 406 VAL GLY PHE LYS THR ALA MET THR ARG VAL PHE ASN ASP SEQRES 24 A 406 TYR ALA ARG ARG ILE ASN GLU LEU LYS THR LYS ASP LYS SEQRES 25 A 406 ASN LEU ASP GLY ASN ASP ILE ARG GLU GLY LEU THR ALA SEQRES 26 A 406 VAL VAL SER VAL ARG ILE PRO GLU GLU LEU LEU GLN PHE SEQRES 27 A 406 GLU GLY GLN THR LYS SER LYS LEU GLY THR SER GLU ALA SEQRES 28 A 406 ARG SER ALA VAL ASP SER VAL VAL ALA ASP LYS LEU PRO SEQRES 29 A 406 PHE TYR LEU GLU GLU LYS GLY GLN LEU SER LYS SER LEU SEQRES 30 A 406 VAL LYS LYS ALA ILE LYS ALA GLN GLN ALA ARG GLU ALA SEQRES 31 A 406 ALA ARG LYS ALA ARG GLU ASP ALA ARG SER GLY LYS LYS SEQRES 32 A 406 ASN LYS ARG SEQRES 1 B 406 MET ALA MET ASN LYS GLN ASN ASN TYR SER ASP ASP SER SEQRES 2 B 406 ILE GLN VAL LEU GLU GLY LEU GLU ALA VAL ARG LYS ARG SEQRES 3 B 406 PRO GLY MET TYR ILE GLY SER THR ASP LYS ARG GLY LEU SEQRES 4 B 406 HIS HIS LEU VAL TYR GLU ILE VAL ASP ASN SER VAL ASP SEQRES 5 B 406 GLU VAL LEU ASN GLY TYR GLY ASN GLU ILE ASP VAL THR SEQRES 6 B 406 ILE ASN LYS ASP GLY SER ILE SER ILE GLU ASP ASN GLY SEQRES 7 B 406 ARG GLY MET PRO THR GLY ILE HIS LYS SER GLY LYS PRO SEQRES 8 B 406 THR VAL GLU VAL ILE PHE THR VAL LEU HIS ALA GLY GLY SEQRES 9 B 406 LYS PHE GLY GLN GLY GLY TYR LYS THR SER GLY GLY LEU SEQRES 10 B 406 HIS GLY VAL GLY ALA SER VAL VAL ASN ALA LEU SER GLU SEQRES 11 B 406 TRP LEU GLU VAL GLU ILE HIS ARG ASP GLY ASN ILE TYR SEQRES 12 B 406 HIS GLN SER PHE LYS ASN GLY GLY SER PRO SER SER GLY SEQRES 13 B 406 LEU VAL LYS LYS GLY LYS THR LYS LYS THR GLY THR LYS SEQRES 14 B 406 VAL THR PHE LYS PRO ASP ASP THR ILE PHE LYS ALA SER SEQRES 15 B 406 THR SER PHE ASN PHE ASP VAL LEU SER GLU ARG LEU GLN SEQRES 16 B 406 GLU SER ALA PHE LEU LEU LYS ASN LEU LYS ILE THR LEU SEQRES 17 B 406 ASN ASP LEU ARG SER GLY LYS GLU ARG GLN GLU HIS TYR SEQRES 18 B 406 HIS TYR GLU GLU GLY ILE LYS GLU PHE VAL SER TYR VAL SEQRES 19 B 406 ASN GLU GLY LYS GLU VAL LEU HIS ASP VAL ALA THR PHE SEQRES 20 B 406 SER GLY GLU ALA ASN GLY ILE GLU VAL ASP VAL ALA PHE SEQRES 21 B 406 GLN TYR ASN ASP GLN TYR SER GLU SER ILE LEU SER PHE SEQRES 22 B 406 VAL ASN ASN VAL ARG THR LYS ASP GLY GLY THR HIS GLU SEQRES 23 B 406 VAL GLY PHE LYS THR ALA MET THR ARG VAL PHE ASN ASP SEQRES 24 B 406 TYR ALA ARG ARG ILE ASN GLU LEU LYS THR LYS ASP LYS SEQRES 25 B 406 ASN LEU ASP GLY ASN ASP ILE ARG GLU GLY LEU THR ALA SEQRES 26 B 406 VAL VAL SER VAL ARG ILE PRO GLU GLU LEU LEU GLN PHE SEQRES 27 B 406 GLU GLY GLN THR LYS SER LYS LEU GLY THR SER GLU ALA SEQRES 28 B 406 ARG SER ALA VAL ASP SER VAL VAL ALA ASP LYS LEU PRO SEQRES 29 B 406 PHE TYR LEU GLU GLU LYS GLY GLN LEU SER LYS SER LEU SEQRES 30 B 406 VAL LYS LYS ALA ILE LYS ALA GLN GLN ALA ARG GLU ALA SEQRES 31 B 406 ALA ARG LYS ALA ARG GLU ASP ALA ARG SER GLY LYS LYS SEQRES 32 B 406 ASN LYS ARG HET XAM A2000 64 HET XAM B2000 64 HETNAM XAM (1R,4AS,5S,6S,8AR)-5-{[(5S)-1-(3-O-ACETYL-4-O- HETNAM 2 XAM CARBAMOYL-6-DEOXY-2-O-METHYL-ALPHA-L-TALOPYRANOSYL)-4- HETNAM 3 XAM HYDROXY-2-OXO-5-(PROPAN-2-YL)-2,5-DIHYDRO-1H-PYRROL-3- HETNAM 4 XAM YL]CARBONYL}-6-METHYL-4-METHYLIDENE-1,2,3,4,4A,5,6,8A- HETNAM 5 XAM OCTAHYDRONAPHTHALEN-1-YL 2,6-DIDEOXY-3-C-[(1S)-1-{[(3, HETNAM 6 XAM 4-DICHLORO-5-METHYL-1H-PYRROL-2-YL) HETNAM 7 XAM CARBONYL]AMINO}ETHYL]-BETA-D-RIBO-HEXOPYRANOSIDE HETSYN XAM AMYCOLAMICIN FORMUL 3 XAM 2(C44 H60 CL2 N4 O14) FORMUL 5 HOH *106(H2 O) HELIX 1 1 GLY A 19 ARG A 26 1 8 HELIX 2 2 PRO A 27 GLY A 32 1 6 HELIX 3 3 ASP A 35 ASN A 56 1 22 HELIX 4 4 PRO A 91 VAL A 99 1 9 HELIX 5 5 GLY A 121 LEU A 128 1 8 HELIX 6 6 ASN A 186 LEU A 201 1 16 HELIX 7 7 GLY A 226 ASN A 235 1 10 HELIX 8 8 GLY A 283 ILE A 304 1 22 HELIX 9 9 ASP A 315 ARG A 320 1 6 HELIX 10 10 SER A 349 SER A 400 1 52 HELIX 11 11 GLU B 21 ARG B 26 1 6 HELIX 12 12 ARG B 26 GLY B 32 1 7 HELIX 13 13 ASP B 35 ASN B 56 1 22 HELIX 14 14 PRO B 91 VAL B 99 1 9 HELIX 15 15 GLY B 121 LEU B 128 1 8 HELIX 16 16 ASN B 186 LEU B 201 1 16 HELIX 17 17 GLY B 226 ASN B 235 1 10 HELIX 18 18 GLY B 283 ILE B 304 1 22 HELIX 19 19 ASP B 315 ARG B 320 1 6 HELIX 20 20 THR B 348 ARG B 399 1 52 SHEET 1 AA 2 SER A 152 PRO A 153 0 SHEET 2 AA 2 ASN A 141 LYS A 148 1 O LYS A 148 N SER A 152 SHEET 1 AB 2 VAL A 158 LYS A 162 0 SHEET 2 AB 2 ASN A 141 LYS A 148 -1 O ILE A 142 N LYS A 160 SHEET 1 AC 8 ARG A 217 HIS A 222 0 SHEET 2 AC 8 LYS A 205 ASP A 210 -1 O ILE A 206 N TYR A 221 SHEET 3 AC 8 GLU A 61 ILE A 66 1 O ILE A 62 N THR A 207 SHEET 4 AC 8 ILE A 72 ASP A 76 -1 O SER A 73 N THR A 65 SHEET 5 AC 8 GLY A 167 PRO A 174 -1 O THR A 168 N ASP A 76 SHEET 6 AC 8 SER A 129 ARG A 138 -1 N GLU A 130 O LYS A 173 SHEET 7 AC 8 ASN A 141 LYS A 148 -1 O ASN A 141 N ARG A 138 SHEET 8 AC 8 SER A 152 PRO A 153 1 O SER A 152 N LYS A 148 SHEET 1 AD 8 ARG A 217 HIS A 222 0 SHEET 2 AD 8 LYS A 205 ASP A 210 -1 O ILE A 206 N TYR A 221 SHEET 3 AD 8 GLU A 61 ILE A 66 1 O ILE A 62 N THR A 207 SHEET 4 AD 8 ILE A 72 ASP A 76 -1 O SER A 73 N THR A 65 SHEET 5 AD 8 GLY A 167 PRO A 174 -1 O THR A 168 N ASP A 76 SHEET 6 AD 8 SER A 129 ARG A 138 -1 N GLU A 130 O LYS A 173 SHEET 7 AD 8 ASN A 141 LYS A 148 -1 O ASN A 141 N ARG A 138 SHEET 8 AD 8 VAL A 158 LYS A 162 -1 O VAL A 158 N HIS A 144 SHEET 1 AE 5 ALA A 245 ALA A 251 0 SHEET 2 AE 5 ILE A 254 TYR A 262 -1 O ILE A 254 N ALA A 251 SHEET 3 AE 5 LEU A 323 ARG A 330 -1 O THR A 324 N GLN A 261 SHEET 4 AE 5 SER A 269 VAL A 274 1 O SER A 269 N ALA A 325 SHEET 5 AE 5 VAL A 277 ARG A 278 -1 O VAL A 277 N VAL A 274 SHEET 1 BA 2 SER B 152 PRO B 153 0 SHEET 2 BA 2 ASN B 141 LYS B 148 1 O LYS B 148 N SER B 152 SHEET 1 BB 2 VAL B 158 LYS B 162 0 SHEET 2 BB 2 ASN B 141 LYS B 148 -1 O ILE B 142 N LYS B 160 SHEET 1 BC 8 ARG B 217 HIS B 222 0 SHEET 2 BC 8 LYS B 205 ASP B 210 -1 O ILE B 206 N TYR B 221 SHEET 3 BC 8 GLU B 61 ILE B 66 1 O ILE B 62 N THR B 207 SHEET 4 BC 8 ILE B 72 ASP B 76 -1 O SER B 73 N THR B 65 SHEET 5 BC 8 GLY B 167 PRO B 174 -1 O THR B 168 N ASP B 76 SHEET 6 BC 8 SER B 129 ARG B 138 -1 N GLU B 130 O LYS B 173 SHEET 7 BC 8 ASN B 141 LYS B 148 -1 O ASN B 141 N ARG B 138 SHEET 8 BC 8 SER B 152 PRO B 153 1 O SER B 152 N LYS B 148 SHEET 1 BD 8 ARG B 217 HIS B 222 0 SHEET 2 BD 8 LYS B 205 ASP B 210 -1 O ILE B 206 N TYR B 221 SHEET 3 BD 8 GLU B 61 ILE B 66 1 O ILE B 62 N THR B 207 SHEET 4 BD 8 ILE B 72 ASP B 76 -1 O SER B 73 N THR B 65 SHEET 5 BD 8 GLY B 167 PRO B 174 -1 O THR B 168 N ASP B 76 SHEET 6 BD 8 SER B 129 ARG B 138 -1 N GLU B 130 O LYS B 173 SHEET 7 BD 8 ASN B 141 LYS B 148 -1 O ASN B 141 N ARG B 138 SHEET 8 BD 8 VAL B 158 LYS B 162 -1 O VAL B 158 N HIS B 144 SHEET 1 BE 5 ALA B 245 ALA B 251 0 SHEET 2 BE 5 ILE B 254 TYR B 262 -1 O ILE B 254 N ALA B 251 SHEET 3 BE 5 LEU B 323 ARG B 330 -1 O THR B 324 N GLN B 261 SHEET 4 BE 5 SER B 269 VAL B 274 1 O SER B 269 N ALA B 325 SHEET 5 BE 5 VAL B 277 ARG B 278 -1 O VAL B 277 N VAL B 274 SITE 1 AC1 18 ASN A 49 SER A 50 GLU A 53 ASP A 76 SITE 2 AC1 18 ARG A 79 MET A 81 PRO A 82 HIS A 86 SITE 3 AC1 18 THR A 92 ILE A 96 LEU A 100 HIS A 101 SITE 4 AC1 18 ALA A 102 GLY A 103 THR A 168 HOH A2004 SITE 5 AC1 18 HOH A2008 HOH A2009 SITE 1 AC2 18 ASN B 49 SER B 50 GLU B 53 ASP B 76 SITE 2 AC2 18 ARG B 79 MET B 81 HIS B 86 LYS B 87 SITE 3 AC2 18 THR B 92 LEU B 100 HIS B 101 ALA B 102 SITE 4 AC2 18 GLY B 103 GLY B 104 THR B 168 HOH B2003 SITE 5 AC2 18 HOH B2007 HOH B2008 CRYST1 54.449 136.809 69.191 90.00 111.92 90.00 P 1 21 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 0.018366 0.000000 0.007390 0.00000 SCALE2 0.000000 0.007309 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015579 0.00000