HEADER SIGNALING PROTEIN 04-SEP-11 3TO5 TITLE HIGH RESOLUTION STRUCTURE OF CHEY3 FROM VIBRIO CHOLERAE COMPND MOL_ID: 1; COMPND 2 MOLECULE: CHEY HOMOLOG; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CHEMOTAXIS PROTEIN CHEY; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VIBRIO CHOLERAE; SOURCE 3 ORGANISM_TAXID: 666; SOURCE 4 GENE: CHEY3, VC_2065; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28A+ KEYWDS ALPHA(5)BETA(5), CHEMOTAXIS, FLIM, PHOSPHORYLATION, MOTOR ACTION, KEYWDS 2 SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.DASGUPTA,U.SEN,M.BISWAS REVDAT 3 01-NOV-23 3TO5 1 REMARK SEQADV LINK REVDAT 2 09-OCT-13 3TO5 1 JRNL REMARK REVDAT 1 12-SEP-12 3TO5 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 2 REMARK 2 RESOLUTION. 1.65 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) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.26 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1223213.730 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 94.3 REMARK 3 NUMBER OF REFLECTIONS : 14876 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) : 0.202 REMARK 3 FREE R VALUE : 0.229 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 764 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.008 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) : 1.65 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.75 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 91.40 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2264 REMARK 3 BIN R VALUE (WORKING SET) : 0.3090 REMARK 3 BIN FREE R VALUE : 0.3240 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.60 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 134 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.028 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 980 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 175 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.62000 REMARK 3 B22 (A**2) : 0.62000 REMARK 3 B33 (A**2) : -1.23000 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) : 0.16 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) : 0.17 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) : 22.40 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.870 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) : 2.200 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 3.430 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 3.560 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 5.570 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.40 REMARK 3 BSOL : 62.45 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 : CIS_PEPTIDE.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : ION.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER_REP.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 3TO5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 15-SEP-11. REMARK 100 THE DEPOSITION ID IS D_1000067712. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-AUG-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 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 RU200 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 : 14876 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 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 (%) : 94.3 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL 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) : 1.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.75 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.4 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: LAUE REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 2CHE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.69 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.22 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 6000, 0.1M TRIS, PH 7.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 X+2/3,Y+1/3,Z+1/3 REMARK 290 5555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 6555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 7555 X+1/3,Y+2/3,Z+2/3 REMARK 290 8555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 9555 -X+Y+1/3,-X+2/3,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 0.00000 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 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 34.02850 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 19.64636 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 25.25000 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 34.02850 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 19.64636 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 25.25000 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 34.02850 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 19.64636 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 25.25000 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 39.29273 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 50.50000 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 39.29273 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 50.50000 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 39.29273 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 50.50000 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 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 -3 REMARK 465 SER A -2 REMARK 465 HIS A -1 REMARK 465 MET A 0 REMARK 465 MET A 1 REMARK 465 GLU A 2 REMARK 465 ALA A 3 REMARK 465 ILE A 4 REMARK 465 ARG A 129 REMARK 465 LEU A 130 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 LEU A 5 CG CD1 CD2 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 131 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 15 OD2 REMARK 620 2 ASP A 16 OD1 72.5 REMARK 620 3 ASP A 60 OD2 77.6 131.8 REMARK 620 4 ASN A 62 O 114.7 82.4 76.8 REMARK 620 5 HOH A 142 O 73.2 95.9 110.7 170.7 REMARK 620 6 HOH A 160 O 135.8 71.2 146.5 84.3 86.4 REMARK 620 7 HOH A 191 O 137.1 144.9 80.6 95.4 80.7 73.8 REMARK 620 N 1 2 3 4 5 6 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 131 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4LX8 RELATED DB: PDB REMARK 900 RELATED ID: 4H60 RELATED DB: PDB REMARK 900 RELATED ID: 4HNQ RELATED DB: PDB REMARK 900 RELATED ID: 4HNR RELATED DB: PDB REMARK 900 RELATED ID: 4HNS RELATED DB: PDB DBREF 3TO5 A 1 130 UNP Q9KQD5 Q9KQD5_VIBCH 1 130 SEQADV 3TO5 GLY A -3 UNP Q9KQD5 EXPRESSION TAG SEQADV 3TO5 SER A -2 UNP Q9KQD5 EXPRESSION TAG SEQADV 3TO5 HIS A -1 UNP Q9KQD5 EXPRESSION TAG SEQADV 3TO5 MET A 0 UNP Q9KQD5 EXPRESSION TAG SEQRES 1 A 134 GLY SER HIS MET MET GLU ALA ILE LEU ASN LYS ASN MET SEQRES 2 A 134 LYS ILE LEU ILE VAL ASP ASP PHE SER THR MET ARG ARG SEQRES 3 A 134 ILE VAL LYS ASN LEU LEU ARG ASP LEU GLY PHE ASN ASN SEQRES 4 A 134 THR GLN GLU ALA ASP ASP GLY LEU THR ALA LEU PRO MET SEQRES 5 A 134 LEU LYS LYS GLY ASP PHE ASP PHE VAL VAL THR ASP TRP SEQRES 6 A 134 ASN MET PRO GLY MET GLN GLY ILE ASP LEU LEU LYS ASN SEQRES 7 A 134 ILE ARG ALA ASP GLU GLU LEU LYS HIS LEU PRO VAL LEU SEQRES 8 A 134 MET ILE THR ALA GLU ALA LYS ARG GLU GLN ILE ILE GLU SEQRES 9 A 134 ALA ALA GLN ALA GLY VAL ASN GLY TYR ILE VAL LYS PRO SEQRES 10 A 134 PHE THR ALA ALA THR LEU LYS GLU LYS LEU ASP LYS ILE SEQRES 11 A 134 PHE GLU ARG LEU HET CA A 131 1 HETNAM CA CALCIUM ION FORMUL 2 CA CA 2+ FORMUL 3 HOH *175(H2 O) HELIX 1 1 PHE A 17 LEU A 31 1 15 HELIX 2 2 ASP A 41 ASP A 53 1 13 HELIX 3 3 GLN A 67 ASP A 78 1 12 HELIX 4 4 LYS A 94 ALA A 104 1 11 HELIX 5 5 THR A 115 PHE A 127 1 13 SHEET 1 A 5 THR A 36 ALA A 39 0 SHEET 2 A 5 ILE A 11 VAL A 14 1 N ILE A 13 O GLN A 37 SHEET 3 A 5 PHE A 56 ASP A 60 1 O VAL A 58 N VAL A 14 SHEET 4 A 5 VAL A 86 THR A 90 1 O LEU A 87 N VAL A 57 SHEET 5 A 5 GLY A 108 VAL A 111 1 O GLY A 108 N MET A 88 LINK OD2 ASP A 15 CA CA A 131 1555 1555 2.52 LINK OD1 ASP A 16 CA CA A 131 1555 1555 2.39 LINK OD2 ASP A 60 CA CA A 131 1555 1555 2.39 LINK O ASN A 62 CA CA A 131 1555 1555 2.38 LINK CA CA A 131 O HOH A 142 1555 1555 2.36 LINK CA CA A 131 O HOH A 160 1555 1555 2.45 LINK CA CA A 131 O HOH A 191 1555 1555 2.42 CISPEP 1 LYS A 112 PRO A 113 0 -0.07 SITE 1 AC1 7 ASP A 15 ASP A 16 ASP A 60 ASN A 62 SITE 2 AC1 7 HOH A 142 HOH A 160 HOH A 191 CRYST1 68.057 68.057 75.750 90.00 90.00 120.00 H 3 9 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 0.014694 0.008483 0.000000 0.00000 SCALE2 0.000000 0.016967 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013201 0.00000