HEADER SIGNALING PROTEIN 19-SEP-12 4H60 TITLE HIGH RESOLUTION STRUCTURE OF VIBRIO CHOLERAE CHEMOTAXIS PROTEIN CHEY4 TITLE 2 CRYSTALLIZED IN LOW PH (4.0) CONDITION COMPND MOL_ID: 1; COMPND 2 MOLECULE: CHEMOTAXIS PROTEIN CHEY; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 7-125; COMPND 5 SYNONYM: CHEY4; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VIBRIO CHOLERAE; SOURCE 3 ORGANISM_TAXID: 345073; SOURCE 4 STRAIN: ATCC 39541 / OGAWA 395 / O395; SOURCE 5 GENE: CHEY-4; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ROSSMANN FOLD, RESPONSE REGULATOR, CHEMOTAXIS, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.BISWAS,J.DASGUPTA,U.SEN REVDAT 4 20-SEP-23 4H60 1 REMARK SEQADV LINK REVDAT 3 20-NOV-13 4H60 1 JRNL REVDAT 2 02-OCT-13 4H60 1 JRNL REVDAT 1 07-AUG-13 4H60 0 JRNL AUTH M.BISWAS,S.DEY,S.KHAMRUI,U.SEN,J.DASGUPTA JRNL TITL CONFORMATIONAL BARRIER OF CHEY3 AND INABILITY OF CHEY4 TO JRNL TITL 2 BIND FLIM CONTROL THE FLAGELLAR MOTOR ACTION IN VIBRIO JRNL TITL 3 CHOLERAE. JRNL REF PLOS ONE V. 8 73923 2013 JRNL REFN ESSN 1932-6203 JRNL PMID 24066084 JRNL DOI 10.1371/JOURNAL.PONE.0073923 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH M.BISWAS,S.KHAMRUI,U.SEN,J.DASGUPTA REMARK 1 TITL OVEREXPRESSION, PURIFICATION, CRYSTALLIZATION AND REMARK 1 TITL 2 PRELIMINARY X-RAY ANALYSIS OF CHEY4 FROM VIBRIO CHOLERAE REMARK 1 TITL 3 O395. REMARK 1 REF ACTA CRYSTALLOGR.,SECT.F V. 67 1645 2011 REMARK 1 REFN ESSN 1744-3091 REMARK 1 PMID 22139188 REMARK 1 DOI 10.1107/S1744309111041972 REMARK 2 REMARK 2 RESOLUTION. 1.66 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.2 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) : 1.66 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 22.24 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 861015.340 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 95.0 REMARK 3 NUMBER OF REFLECTIONS : 10882 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) : 0.218 REMARK 3 FREE R VALUE : 0.246 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 548 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.010 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) : 1.66 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.76 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.10 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1647 REMARK 3 BIN R VALUE (WORKING SET) : 0.3920 REMARK 3 BIN FREE R VALUE : 0.3220 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.70 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 100 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.032 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 930 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 6 REMARK 3 SOLVENT ATOMS : 113 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.30 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.96000 REMARK 3 B22 (A**2) : -1.96000 REMARK 3 B33 (A**2) : 1.00000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -2.63000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.22 REMARK 3 ESD FROM SIGMAA (A) : 0.19 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) : 0.24 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.18 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.021 REMARK 3 BOND ANGLES (DEGREES) : 1.500 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.20 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.230 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) : 2.020 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 3.150 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 4.940 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 7.500 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.40 REMARK 3 BSOL : 44.73 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 : ION.PARAM REMARK 3 PARAMETER FILE 4 : CIS_PEPTIDE.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : ION.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED REMARK 4 REMARK 4 4H60 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-SEP-12. REMARK 100 THE DEPOSITION ID IS D_1000075062. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JAN-04 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU300 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : AUTOMAR REMARK 200 DATA SCALING SOFTWARE : AUTOMAR REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10882 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.660 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.1 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.04490 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.66 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 3TO5 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 31.96 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.81 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.6 M AMMONIUM SULFATE, PH 4.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 47.64550 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 15.50700 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 47.64550 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 15.50700 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 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 SER A 86 CB SER A 86 OG -0.094 REMARK 500 PRO A 87 C PRO A 87 O -0.120 REMARK 500 VAL A 96 CB VAL A 96 CG1 -0.201 REMARK 500 VAL A 96 CB VAL A 96 CG2 -0.230 REMARK 500 VAL A 96 C VAL A 96 O -0.146 REMARK 500 ASN A 107 C ASN A 107 O -0.153 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 VAL A 57 -90.40 -102.93 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 201 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 9 OD1 REMARK 620 2 ASP A 52 OD2 91.4 REMARK 620 3 ASN A 54 O 104.5 78.3 REMARK 620 4 HOH A 368 O 87.8 95.9 166.3 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 202 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3TO5 RELATED DB: PDB DBREF 4H60 A 1 119 UNP C3M734 C3M734_VIBC3 7 125 SEQADV 4H60 ALA A -1 UNP C3M734 EXPRESSION TAG SEQRES 1 A 120 ALA MET ALA LYS VAL LEU ALA VAL ASP ASP SER ILE SER SEQRES 2 A 120 ILE ARG GLN MET VAL SER HIS THR LEU GLN ASP ALA GLY SEQRES 3 A 120 TYR GLU VAL GLU THR ALA ALA ASP GLY ARG GLU ALA LEU SEQRES 4 A 120 ALA LYS ALA GLN LYS ALA ARG PHE ASP VAL ILE ILE SER SEQRES 5 A 120 ASP VAL ASN MET PRO VAL MET THR GLY PHE GLU PHE VAL SEQRES 6 A 120 LYS ALA VAL ARG MET GLN SER GLN TYR LYS PHE THR PRO SEQRES 7 A 120 ILE LEU MET LEU THR THR GLU THR SER PRO GLU LYS LYS SEQRES 8 A 120 GLN GLU GLY LYS ALA VAL GLY ALA THR GLY TRP LEU VAL SEQRES 9 A 120 LYS PRO PHE ASN PRO GLU THR LEU LEU LYS THR LEU GLN SEQRES 10 A 120 ARG VAL LEU HET CA A 201 1 HET SO4 A 202 5 HETNAM CA CALCIUM ION HETNAM SO4 SULFATE ION FORMUL 2 CA CA 2+ FORMUL 3 SO4 O4 S 2- FORMUL 4 HOH *113(H2 O) HELIX 1 1 SER A 10 GLY A 25 1 16 HELIX 2 2 ASP A 33 ALA A 44 1 12 HELIX 3 3 THR A 59 ARG A 68 1 10 HELIX 4 4 MET A 69 LYS A 74 5 6 HELIX 5 5 SER A 86 GLY A 97 1 12 HELIX 6 6 ASN A 107 LEU A 119 1 13 SHEET 1 A 5 GLU A 27 ALA A 31 0 SHEET 2 A 5 LYS A 3 VAL A 7 1 N VAL A 4 O GLU A 27 SHEET 3 A 5 VAL A 48 ASP A 52 1 O ILE A 50 N VAL A 7 SHEET 4 A 5 ILE A 78 THR A 82 1 O LEU A 79 N SER A 51 SHEET 5 A 5 GLY A 100 VAL A 103 1 O GLY A 100 N MET A 80 LINK OD1 ASP A 9 CA CA A 201 1555 1555 2.62 LINK OD2 ASP A 52 CA CA A 201 1555 1555 2.25 LINK O ASN A 54 CA CA A 201 1555 1555 2.25 LINK CA CA A 201 O HOH A 368 1555 1555 2.33 CISPEP 1 LYS A 104 PRO A 105 0 -1.52 SITE 1 AC1 5 ASP A 9 ASP A 52 ASN A 54 SO4 A 202 SITE 2 AC1 5 HOH A 368 SITE 1 AC2 8 ASP A 52 VAL A 53 ASN A 54 THR A 82 SITE 2 AC2 8 THR A 83 LYS A 104 CA A 201 HOH A 392 CRYST1 95.291 31.014 32.735 90.00 96.59 90.00 C 1 2 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 0.010494 0.000000 0.001212 0.00000 SCALE2 0.000000 0.032244 0.000000 0.00000 SCALE3 0.000000 0.000000 0.030751 0.00000