HEADER UNKNOWN FUNCTION 12-SEP-01 1JYH TITLE CRYSTAL STRUCTURE OF THE ESCHERICHIA COLI SBMC PROTEIN (AKA GYRASE TITLE 2 INHIBITORY PROTEIN GYRI, AKA YEEB) COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA GYRASE INHIBITORY PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: GYRASE INHIBITORY PROTEIN GYRI; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: GYRI (SBMC,YEEB); SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PGEX6P-1 KEYWDS GYRASE INHIBITOR, STRUCTURAL GENOMICS, PSI, PROTEIN STRUCTURE KEYWDS 2 INITIATIVE, NEW YORK SGX RESEARCH CENTER FOR STRUCTURAL GENOMICS, KEYWDS 3 NYSGXRC, UNKNOWN FUNCTION EXPDTA X-RAY DIFFRACTION AUTHOR M.J.ROMANOWSKI,S.A.GIBNEY,S.K.BURLEY,NEW YORK SGX RESEARCH CENTER FOR AUTHOR 2 STRUCTURAL GENOMICS (NYSGXRC) REVDAT 6 07-FEB-24 1JYH 1 REMARK REVDAT 5 03-FEB-21 1JYH 1 AUTHOR JRNL REVDAT 4 24-FEB-09 1JYH 1 VERSN REVDAT 3 25-JAN-05 1JYH 1 AUTHOR KEYWDS REMARK REVDAT 2 24-APR-02 1JYH 1 COMPND REVDAT 1 10-APR-02 1JYH 0 JRNL AUTH M.J.ROMANOWSKI,S.A.GIBNEY,S.K.BURLEY JRNL TITL CRYSTAL STRUCTURE OF THE ESCHERICHIA COLI SBMC PROTEIN THAT JRNL TITL 2 PROTECTS CELLS FROM THE DNA REPLICATION INHIBITOR MICROCIN JRNL TITL 3 B17. JRNL REF PROTEINS V. 47 403 2002 JRNL REFN ISSN 0887-3585 JRNL PMID 11948793 JRNL DOI 10.1002/PROT.10102 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 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 : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.93 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 839905.220 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 95.7 REMARK 3 NUMBER OF REFLECTIONS : 19658 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) : 0.196 REMARK 3 FREE R VALUE : 0.222 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1932 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 : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.91 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.90 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2911 REMARK 3 BIN R VALUE (WORKING SET) : 0.1870 REMARK 3 BIN FREE R VALUE : 0.2390 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.10 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 326 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.013 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1256 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 177 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 10.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.37000 REMARK 3 B22 (A**2) : 0.37000 REMARK 3 B33 (A**2) : -0.75000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.19 REMARK 3 ESD FROM SIGMAA (A) : -0.0 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) : 0.22 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.04 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.00 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.670 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) : 1.180 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.820 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.030 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.040 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.45 REMARK 3 BSOL : 56.69 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 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1JYH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-SEP-01. REMARK 100 THE DEPOSITION ID IS D_1000014333. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-AUG-01; 08-AUG-01 REMARK 200 TEMPERATURE (KELVIN) : 100; 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : NSLS; NSLS REMARK 200 BEAMLINE : X9A; X9A REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97935, 0.97954; 0.97962 REMARK 200 MONOCHROMATOR : SI 111; SI 111 REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD; CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH; MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19658 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.7 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.05700 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) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.3 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.09000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD; SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: MLPHARE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.02 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.93 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG2000 MONOMETHYL ETHER, AMMONIUM REMARK 280 SULFATE, SODIUM ACETATE, PH 4.6, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 40.44550 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 36.22000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 36.22000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 60.66825 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 36.22000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 36.22000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 20.22275 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 36.22000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 36.22000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 60.66825 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 36.22000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 36.22000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 20.22275 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 40.44550 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: MONOMERIC 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 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 HIS A 156 REMARK 465 HIS A 157 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 81 54.03 -118.84 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: NYSGXRC-T473 RELATED DB: TARGETDB DBREF 1JYH A 1 157 UNP P33012 GYRI_ECOLI 1 157 SEQRES 1 A 157 MET ASN TYR GLU ILE LYS GLN GLU GLU LYS ARG THR VAL SEQRES 2 A 157 ALA GLY PHE HIS LEU VAL GLY PRO TRP GLU GLN THR VAL SEQRES 3 A 157 LYS LYS GLY PHE GLU GLN LEU MET MET TRP VAL ASP SER SEQRES 4 A 157 LYS ASN ILE VAL PRO LYS GLU TRP VAL ALA VAL TYR TYR SEQRES 5 A 157 ASP ASN PRO ASP GLU THR PRO ALA GLU LYS LEU ARG CYS SEQRES 6 A 157 ASP THR VAL VAL THR VAL PRO GLY TYR PHE THR LEU PRO SEQRES 7 A 157 GLU ASN SER GLU GLY VAL ILE LEU THR GLU ILE THR GLY SEQRES 8 A 157 GLY GLN TYR ALA VAL ALA VAL ALA ARG VAL VAL GLY ASP SEQRES 9 A 157 ASP PHE ALA LYS PRO TRP TYR GLN PHE PHE ASN SER LEU SEQRES 10 A 157 LEU GLN ASP SER ALA TYR GLU MET LEU PRO LYS PRO CYS SEQRES 11 A 157 PHE GLU VAL TYR LEU ASN ASN GLY ALA GLU ASP GLY TYR SEQRES 12 A 157 TRP ASP ILE GLU MET TYR VAL ALA VAL GLN PRO LYS HIS SEQRES 13 A 157 HIS FORMUL 2 HOH *177(H2 O) HELIX 1 1 PRO A 21 LYS A 40 1 20 HELIX 2 2 PRO A 59 LYS A 62 5 4 HELIX 3 3 PHE A 106 LEU A 118 1 13 HELIX 4 4 ASN A 137 GLY A 142 1 6 SHEET 1 A 4 GLU A 4 GLU A 8 0 SHEET 2 A 4 GLY A 92 VAL A 101 -1 O TYR A 94 N LYS A 6 SHEET 3 A 4 TRP A 144 PRO A 154 -1 O VAL A 150 N ALA A 95 SHEET 4 A 4 TYR A 123 MET A 125 -1 N GLU A 124 O GLN A 153 SHEET 1 B 8 GLU A 4 GLU A 8 0 SHEET 2 B 8 GLY A 92 VAL A 101 -1 O TYR A 94 N LYS A 6 SHEET 3 B 8 TRP A 144 PRO A 154 -1 O VAL A 150 N ALA A 95 SHEET 4 B 8 CYS A 130 TYR A 134 -1 N PHE A 131 O TYR A 149 SHEET 5 B 8 GLU A 46 TYR A 51 -1 N TYR A 51 O CYS A 130 SHEET 6 B 8 ARG A 64 VAL A 71 -1 O VAL A 68 N VAL A 48 SHEET 7 B 8 ARG A 11 VAL A 19 -1 N LEU A 18 O CYS A 65 SHEET 8 B 8 ILE A 85 ILE A 89 -1 O ILE A 85 N GLY A 15 CRYST1 72.440 72.440 80.891 90.00 90.00 90.00 P 43 21 2 8 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 0.013805 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013805 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012362 0.00000