HEADER ANTIBIOTIC INHIBITOR 28-JUN-99 1QTO TITLE 1.5 A CRYSTAL STRUCTURE OF A BLEOMYCIN RESISTANCE DETERMINANT FROM TITLE 2 BLEOMYCIN-PRODUCING STREPTOMYCES VERTICILLUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: BLEOMYCIN-BINDING PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOMYCES VERTICILLUS; SOURCE 3 ORGANISM_TAXID: 29309; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_VECTOR: PKKTRP KEYWDS ARM-EXCHANGE, ANTIBIOTIC INHIBITOR EXPDTA X-RAY DIFFRACTION AUTHOR Y.KAWANO,T.KUMAGAI,K.MUTA,Y.MATOBA,J.DAVIES,M.SUGIYAMA REVDAT 6 14-FEB-24 1QTO 1 REMARK REVDAT 5 04-OCT-17 1QTO 1 REMARK REVDAT 4 16-NOV-11 1QTO 1 HETATM REVDAT 3 13-JUL-11 1QTO 1 VERSN REVDAT 2 24-FEB-09 1QTO 1 VERSN REVDAT 1 28-JUN-00 1QTO 0 JRNL AUTH Y.KAWANO,T.KUMAGAI,K.MUTA,Y.MATOBA,J.DAVIES,M.SUGIYAMA JRNL TITL THE 1.5 A CRYSTAL STRUCTURE OF A BLEOMYCIN RESISTANCE JRNL TITL 2 DETERMINANT FROM BLEOMYCIN-PRODUCING STREPTOMYCES JRNL TITL 3 VERTICILLUS. JRNL REF J.MOL.BIOL. V. 295 915 2000 JRNL REFN ISSN 0022-2836 JRNL PMID 10656800 JRNL DOI 10.1006/JMBI.1999.3404 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH M.SUGIYAMA,C.J.THOMPSON,T.KUMAGAI,K.SUZUKI,R.DEBLAERE, REMARK 1 AUTH 2 R.VILLARROEL,J.DAVIES REMARK 1 TITL CHARACTERISATION BY MOLECULAR CLONING OF TWO GENES FROM REMARK 1 TITL 2 STREPTOMYCES VERTICILLUS ENCODING RESISTANCE TO BLEOMYCIN REMARK 1 REF GENE V. 151 11 1994 REMARK 1 REFN ISSN 0378-1119 REMARK 1 DOI 10.1016/0378-1119(94)90626-2 REMARK 1 REFERENCE 2 REMARK 1 AUTH M.SUGIYAMA,T.KUMAGAI,H.MATSUO,M.Z.A.BHUIYAN,K.UEDA, REMARK 1 AUTH 2 H.MOCHIZUKI,N.NAKAMURA,J.DAVIES REMARK 1 TITL OVERPRODUCTION OF THE BLEOMYCIN-BINDING PROTEINS FROM REMARK 1 TITL 2 BLEOMYCIN-PRODUCING STREPTOMYCES VERTICILLUS AND A REMARK 1 TITL 3 METHICILLIN-RESISTANT STAPHYLOCOCCUS AUREUS IN ESCHERICHIA REMARK 1 TITL 4 COLI AND THEIR IMMUNOLOGICAL CHARACTERISATION REMARK 1 REF FEBS LETT. V. 362 80 1995 REMARK 1 REFN ISSN 0014-5793 REMARK 1 DOI 10.1016/0014-5793(95)00218-X REMARK 1 REFERENCE 3 REMARK 1 AUTH T.KUMAGAI,K.MUTA,Y.MATOBA,Y.KAWANO,N.KAMIYA,J.DAVIES, REMARK 1 AUTH 2 M.SUGIYAMA REMARK 1 TITL CRYSTALLIZATION AND PRELIMINARY X-RAY DIFFRACTION STUDIES OF REMARK 1 TITL 2 BLEOMYCIN-BINDING PROTEIN FROM BLEOMYCIN-PRODUCING REMARK 1 TITL 3 STREPTOMYCES VERTICILLUS REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. 54 127 1998 REMARK 1 REFN ISSN 0907-4449 REMARK 1 DOI 10.1107/S0907444997008871 REMARK 1 REFERENCE 4 REMARK 1 AUTH T.KUMAGAI,T.NAKANO,M.MARUYAMA,H.MOCHIZUKI,M.SUGIYAMA REMARK 1 TITL CHARACTERIZATION OF THE BLEOMYCIN RESISTANCE DETERMINANT REMARK 1 TITL 2 ENCODED ON THE TRANSPOSON TN5 REMARK 1 REF FEBS LETT. V. 442 34 1999 REMARK 1 REFN ISSN 0014-5793 REMARK 1 DOI 10.1016/S0014-5793(98)01613-5 REMARK 1 REFERENCE 5 REMARK 1 AUTH T.KUMAGAI,R.HIBINO,Y.KAWANO,M.SUGIYAMA REMARK 1 TITL MUTATION OF THE N-TERMINAL PROLINE 9 OF BLMA FROM REMARK 1 TITL 2 STREPTOMYCES VERTICILLUS ABOLISHES THE BINDING AFFINITY FOR REMARK 1 TITL 3 BLEOMYCIN REMARK 1 REF FEBS LETT. V. 450 227 1999 REMARK 1 REFN ISSN 0014-5793 REMARK 1 DOI 10.1016/S0014-5793(99)00478-0 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1000000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0010 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 93.9 REMARK 3 NUMBER OF REFLECTIONS : 20570 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) : 0.190 REMARK 3 FREE R VALUE : 0.221 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.800 REMARK 3 FREE R VALUE TEST SET COUNT : 2021 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.005 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.55 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 84.90 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1651 REMARK 3 BIN R VALUE (WORKING SET) : 0.2830 REMARK 3 BIN FREE R VALUE : 0.2630 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.70 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 178 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.020 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 934 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 91 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.17 REMARK 3 ESD FROM SIGMAA (A) : 0.13 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) : 0.18 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.10 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.240 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 26.90 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.650 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) : 1.450 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.500 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.460 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 4.050 ; 2.500 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PRO REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1QTO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-JUN-99. REMARK 100 THE DEPOSITION ID IS D_1000009254. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-MAY-96; 14-NOV-96 REMARK 200 TEMPERATURE (KELVIN) : 298; 298 REMARK 200 PH : 5.7 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY; PHOTON FACTORY REMARK 200 BEAMLINE : BL-6B; BL-6A REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; NULL REMARK 200 WAVELENGTH OR RANGE (A) : 1.0; 1.0 REMARK 200 MONOCHROMATOR : NULL; NULL REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : DIFFRACTOMETER; DIFFRACTOMETER REMARK 200 DETECTOR MANUFACTURER : WEISSENBERG; WEISSENBERG REMARK 200 INTENSITY-INTEGRATION SOFTWARE : WEIS REMARK 200 DATA SCALING SOFTWARE : CCP4 (AGROVATA, ROTAVATA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 74090 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 67.420 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 263.620 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.3 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.05400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.9500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.58 REMARK 200 COMPLETENESS FOR SHELL (%) : 85.7 REMARK 200 DATA REDUNDANCY IN SHELL : 2.70 REMARK 200 R MERGE FOR SHELL (I) : 0.13900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SIRAS REMARK 200 SOFTWARE USED: DM REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.51 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NH4-ACETATE, NA-ACETATE, PEG4000, PH REMARK 280 5.7, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 27.47000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.94000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.47000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 33.94000 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: THE BIOLOGICAL ASSEMBLY IS A HOMODIMER. 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 3120 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11450 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -25.0 KCAL/MOL 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 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 209 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 226 LIES ON A SPECIAL POSITION. 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 85 75.80 -100.39 REMARK 500 REMARK 500 REMARK: NULL DBREF 1QTO A 1 122 UNP Q53793 Q53793_9ACTO 1 122 SEQRES 1 A 122 MET VAL LYS PHE LEU GLY ALA VAL PRO VAL LEU THR ALA SEQRES 2 A 122 VAL ASP VAL PRO ALA ASN VAL SER PHE TRP VAL ASP THR SEQRES 3 A 122 LEU GLY PHE GLU LYS ASP PHE GLY ASP ARG ASP PHE ALA SEQRES 4 A 122 GLY VAL ARG ARG GLY ASP ILE ARG LEU HIS ILE SER ARG SEQRES 5 A 122 THR GLU HIS GLN ILE VAL ALA ASP ASN THR SER ALA TRP SEQRES 6 A 122 ILE GLU VAL THR ASP PRO ASP ALA LEU HIS GLU GLU TRP SEQRES 7 A 122 ALA ARG ALA VAL SER THR ASP TYR ALA ASP THR SER GLY SEQRES 8 A 122 PRO ALA MET THR PRO VAL GLY GLU SER PRO ALA GLY ARG SEQRES 9 A 122 GLU PHE ALA VAL ARG ASP PRO ALA GLY ASN CYS VAL HIS SEQRES 10 A 122 PHE THR ALA GLY GLU FORMUL 2 HOH *91(H2 O) HELIX 1 1 ASP A 15 THR A 26 1 12 HELIX 2 2 HIS A 55 ASP A 60 1 6 HELIX 3 3 ASP A 70 ALA A 79 1 10 SHEET 1 A 4 VAL A 10 ALA A 13 0 SHEET 2 A 4 ILE A 46 ARG A 52 1 O HIS A 49 N LEU A 11 SHEET 3 A 4 PHE A 38 ARG A 43 -1 O ALA A 39 N ILE A 50 SHEET 4 A 4 GLU A 30 GLY A 34 -1 N GLU A 30 O ARG A 42 SHEET 1 B 4 SER A 63 VAL A 68 0 SHEET 2 B 4 CYS A 115 ALA A 120 1 O CYS A 115 N ALA A 64 SHEET 3 B 4 GLY A 103 ARG A 109 -1 O ARG A 104 N ALA A 120 SHEET 4 B 4 ALA A 93 MET A 94 -1 O ALA A 93 N ARG A 109 SHEET 1 B1 4 SER A 63 VAL A 68 0 SHEET 2 B1 4 CYS A 115 ALA A 120 1 O CYS A 115 N ALA A 64 SHEET 3 B1 4 GLY A 103 ARG A 109 -1 O ARG A 104 N ALA A 120 SHEET 4 B1 4 GLY A 98 SER A 100 -1 N GLY A 98 O GLU A 105 CRYST1 54.940 67.880 35.610 90.00 90.00 90.00 P 21 21 2 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 0.018202 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014732 0.000000 0.00000 SCALE3 0.000000 0.000000 0.028082 0.00000