HEADER CELL CYCLE 26-NOV-09 3KU7
TITLE CRYSTAL STRUCTURE OF HELICOBACTER PYLORI MINE, A CELL DIVISION
TITLE 2 TOPOLOGICAL SPECIFICITY FACTOR
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: CELL DIVISION TOPOLOGICAL SPECIFICITY FACTOR;
COMPND 3 CHAIN: A, B;
COMPND 4 SYNONYM: MINE;
COMPND 5 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HELICOBACTER PYLORI;
SOURCE 3 ORGANISM_COMMON: CAMPYLOBACTER PYLORI;
SOURCE 4 ORGANISM_TAXID: 210;
SOURCE 5 GENE: MINE;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID
KEYWDS HELICOBACTER PYLORI, MINE, CELL DIVISION, CELL CYCLE
EXPDTA X-RAY DIFFRACTION
AUTHOR G.B.KANG,H.E.SONG,M.K.KIM,S.H.EOM
REVDAT 3 20-MAR-24 3KU7 1 SEQADV
REVDAT 2 12-FEB-14 3KU7 1 JRNL VERSN
REVDAT 1 05-MAY-10 3KU7 0
JRNL AUTH G.B.KANG,H.E.SONG,M.K.KIM,H.S.YOUN,J.G.LEE,J.Y.AN,J.S.CHUN,
JRNL AUTH 2 H.JEON,S.H.EOM
JRNL TITL CRYSTAL STRUCTURE OF HELICOBACTER PYLORI MINE, A CELL
JRNL TITL 2 DIVISION TOPOLOGICAL SPECIFICITY FACTOR
JRNL REF MOL.MICROBIOL. V. 76 1222 2010
JRNL REFN ISSN 0950-382X
JRNL PMID 20398219
JRNL DOI 10.1111/J.1365-2958.2010.07160.X
REMARK 2
REMARK 2 RESOLUTION. 2.80 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 : MAXIMUM LIKELIHOOD
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.80
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.78
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL
REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL
REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL
REMARK 3 NUMBER OF REFLECTIONS : 4582
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 CROSS-VALIDATION METHOD : NULL
REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM
REMARK 3 R VALUE (WORKING SET) : 0.268
REMARK 3 FREE R VALUE : 0.298
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.900
REMARK 3 FREE R VALUE TEST SET COUNT : 510
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 : NULL
REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.80
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.98
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL
REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL
REMARK 3 BIN R VALUE (WORKING SET) : 0.3520
REMARK 3 BIN FREE R VALUE : 0.3540
REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL
REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL
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 : 972
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 0
REMARK 3 SOLVENT ATOMS : 0
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 64.66
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -6.75100
REMARK 3 B22 (A**2) : -6.75100
REMARK 3 B33 (A**2) : 13.50200
REMARK 3 B12 (A**2) : -19.81900
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) : NULL
REMARK 3 ESD FROM SIGMAA (A) : NULL
REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL
REMARK 3
REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR.
REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL
REMARK 3 ESD FROM C-V SIGMAA (A) : NULL
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES.
REMARK 3 BOND LENGTHS (A) : 0.012
REMARK 3 BOND ANGLES (DEGREES) : 1.800
REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL
REMARK 3 IMPROPER ANGLES (DEGREES) : NULL
REMARK 3
REMARK 3 ISOTROPIC THERMAL MODEL : NULL
REMARK 3
REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA
REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL
REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL
REMARK 3
REMARK 3 BULK SOLVENT MODELING.
REMARK 3 METHOD USED : NULL
REMARK 3 KSOL : NULL
REMARK 3 BSOL : 45.06
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 : NULL
REMARK 3 TOPOLOGY FILE 1 : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 3KU7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 04-DEC-09.
REMARK 100 THE DEPOSITION ID IS D_1000056452.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 17-OCT-07; NULL
REMARK 200 TEMPERATURE (KELVIN) : 100; 100
REMARK 200 PH : 6.5
REMARK 200 NUMBER OF CRYSTALS USED : 2
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y; Y
REMARK 200 RADIATION SOURCE : PAL/PLS; PHOTON FACTORY
REMARK 200 BEAMLINE : 4A; BL-5A
REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000; 0.97964, 0.97912,
REMARK 200 0.98325, 0.96440
REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL MONOCHROMATOR;
REMARK 200 NULL
REMARK 200 OPTICS : NULL; NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD; CCD
REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315; ADSC QUANTUM
REMARK 200 315
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000
REMARK 200 DATA SCALING SOFTWARE : HKL-2000
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4582
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800
REMARK 200 RESOLUTION RANGE LOW (A) : 50.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7
REMARK 200 DATA REDUNDANCY : NULL
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.85
REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0
REMARK 200 DATA REDUNDANCY IN SHELL : NULL
REMARK 200 R MERGE FOR SHELL (I) : NULL
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; MAD
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD
REMARK 200 SOFTWARE USED: SOLVE
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 52.22
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.57
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM MES-NAOH (PH 6.5), 26% (W/V) PEG
REMARK 280 3350, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 64
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 4555 -X,-Y,Z
REMARK 290 5555 Y,-X+Y,Z+1/3
REMARK 290 6555 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 21.83633
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 43.67267
REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 21.83633
REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 43.67267
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: DIMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 2160 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 7280 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -18.0 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 GLY A -2
REMARK 465 SER A -1
REMARK 465 HIS A 0
REMARK 465 MET A 1
REMARK 465 SER A 2
REMARK 465 LEU A 3
REMARK 465 PHE A 4
REMARK 465 ASP A 5
REMARK 465 PHE A 6
REMARK 465 PHE A 7
REMARK 465 LYS A 8
REMARK 465 ASN A 9
REMARK 465 LYS A 10
REMARK 465 GLY A 11
REMARK 465 SER A 12
REMARK 465 ASP A 61
REMARK 465 SER A 62
REMARK 465 ASN A 63
REMARK 465 ARG A 77
REMARK 465 GLY B -2
REMARK 465 SER B -1
REMARK 465 HIS B 0
REMARK 465 MET B 1
REMARK 465 SER B 2
REMARK 465 LEU B 3
REMARK 465 PHE B 4
REMARK 465 ASP B 5
REMARK 465 PHE B 6
REMARK 465 PHE B 7
REMARK 465 LYS B 8
REMARK 465 ASN B 9
REMARK 465 LYS B 10
REMARK 465 GLY B 11
REMARK 465 SER B 12
REMARK 465 ALA B 13
REMARK 465 ALA B 14
REMARK 465 THR B 15
REMARK 465 ASP B 61
REMARK 465 SER B 62
REMARK 465 ASN B 63
REMARK 465 GLN B 64
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 THR A 15 -54.52 -164.14
REMARK 500 THR A 17 111.55 83.51
REMARK 500 LEU A 30 149.56 -39.47
REMARK 500 ASN A 31 -97.22 -82.86
REMARK 500 LEU A 32 85.85 61.08
REMARK 500 LYS A 51 11.88 56.62
REMARK 500 THR A 59 -69.93 -104.48
REMARK 500 LEU B 30 126.15 -39.20
REMARK 500 GLU B 36 80.67 70.43
REMARK 500 GLU B 37 -49.78 153.85
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 3MCD RELATED DB: PDB
DBREF 3KU7 A 1 77 UNP O25099 MINE_HELPY 1 77
DBREF 3KU7 B 1 77 UNP O25099 MINE_HELPY 1 77
SEQADV 3KU7 GLY A -2 UNP O25099 EXPRESSION TAG
SEQADV 3KU7 SER A -1 UNP O25099 EXPRESSION TAG
SEQADV 3KU7 HIS A 0 UNP O25099 EXPRESSION TAG
SEQADV 3KU7 GLY B -2 UNP O25099 EXPRESSION TAG
SEQADV 3KU7 SER B -1 UNP O25099 EXPRESSION TAG
SEQADV 3KU7 HIS B 0 UNP O25099 EXPRESSION TAG
SEQRES 1 A 80 GLY SER HIS MET SER LEU PHE ASP PHE PHE LYS ASN LYS
SEQRES 2 A 80 GLY SER ALA ALA THR ALA THR ASP ARG LEU LYS LEU ILE
SEQRES 3 A 80 LEU ALA LYS GLU ARG THR LEU ASN LEU PRO TYR MET GLU
SEQRES 4 A 80 GLU MET ARG LYS GLU ILE ILE ALA VAL ILE GLN LYS TYR
SEQRES 5 A 80 THR LYS SER SER ASP ILE HIS PHE LYS THR LEU ASP SER
SEQRES 6 A 80 ASN GLN SER VAL GLU THR ILE GLU VAL GLU ILE ILE LEU
SEQRES 7 A 80 PRO ARG
SEQRES 1 B 80 GLY SER HIS MET SER LEU PHE ASP PHE PHE LYS ASN LYS
SEQRES 2 B 80 GLY SER ALA ALA THR ALA THR ASP ARG LEU LYS LEU ILE
SEQRES 3 B 80 LEU ALA LYS GLU ARG THR LEU ASN LEU PRO TYR MET GLU
SEQRES 4 B 80 GLU MET ARG LYS GLU ILE ILE ALA VAL ILE GLN LYS TYR
SEQRES 5 B 80 THR LYS SER SER ASP ILE HIS PHE LYS THR LEU ASP SER
SEQRES 6 B 80 ASN GLN SER VAL GLU THR ILE GLU VAL GLU ILE ILE LEU
SEQRES 7 B 80 PRO ARG
HELIX 1 1 TYR A 34 LYS A 51 1 18
HELIX 2 2 GLU B 37 LYS B 51 1 15
SHEET 1 A 6 ASP A 54 LYS A 58 0
SHEET 2 A 6 VAL A 66 ILE A 74 -1 O GLU A 72 N HIS A 56
SHEET 3 A 6 ARG A 19 GLU A 27 -1 N LEU A 20 O ILE A 73
SHEET 4 A 6 ARG B 19 LYS B 26 -1 O ALA B 25 N LYS A 21
SHEET 5 A 6 GLU B 67 ILE B 74 -1 O ILE B 73 N LEU B 20
SHEET 6 A 6 ASP B 54 LEU B 60 -1 N HIS B 56 O GLU B 72
CRYST1 70.840 70.840 65.509 90.00 90.00 120.00 P 64 12
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 0.014116 0.008150 0.000000 0.00000
SCALE2 0.000000 0.016300 0.000000 0.00000
SCALE3 0.000000 0.000000 0.015265 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
