HEADER DNA BINDING PROTEIN 06-JUN-19 6P7T TITLE CRYSTAL STRUCTURE OF APO TOXT K231A FROM VIBRIO CHOLERAE STRAIN SCE256 COMPND MOL_ID: 1; COMPND 2 MOLECULE: TOXIN CO-REGULATED PILUS VIRULENCE REGULATORY PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VIBRIO CHOLERAE; SOURCE 3 ORGANISM_TAXID: 666; SOURCE 4 GENE: TCPN; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ARAC, XYLS, VIRULENCE REGULATION, CHOLERAE, DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.T.CRUITE,F.J.KULL REVDAT 2 13-MAR-24 6P7T 1 REMARK REVDAT 1 01-JAN-20 6P7T 0 JRNL AUTH J.T.CRUITE,G.KOVACIKOVA,K.A.CLARK,A.K.WOODBREY,K.SKORUPSKI, JRNL AUTH 2 F.J.KULL JRNL TITL STRUCTURAL BASIS FOR VIRULENCE REGULATION INVIBRIO JRNL TITL 2 CHOLERAEBY UNSATURATED FATTY ACID COMPONENTS OF BILE. JRNL REF COMMUN BIOL V. 2 440 2019 JRNL REFN ESSN 2399-3642 JRNL PMID 31815195 JRNL DOI 10.1038/S42003-019-0686-X REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.13_2998 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.55 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.280 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 9664 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.250 REMARK 3 R VALUE (WORKING SET) : 0.246 REMARK 3 FREE R VALUE : 0.287 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.010 REMARK 3 FREE R VALUE TEST SET COUNT : 967 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 28.3873 - 4.7758 1.00 1297 145 0.2162 0.2310 REMARK 3 2 4.7758 - 3.7936 1.00 1226 136 0.2131 0.2788 REMARK 3 3 3.7936 - 3.3149 1.00 1240 138 0.2601 0.3101 REMARK 3 4 3.3149 - 3.0122 1.00 1244 138 0.3051 0.3291 REMARK 3 5 3.0122 - 2.7965 1.00 1248 138 0.3165 0.4097 REMARK 3 6 2.7965 - 2.6317 1.00 1213 135 0.3256 0.3813 REMARK 3 7 2.6317 - 2.5000 1.00 1229 137 0.3532 0.3636 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.440 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 34.000 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 71.58 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 80.83 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6P7T COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-JUN-19. REMARK 100 THE DEPOSITION ID IS D_1000242067. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-JUN-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS-II REMARK 200 BEAMLINE : 17-ID-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9665 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 26.550 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 6.700 REMARK 200 R MERGE (I) : 0.08283 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.3500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.59 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 6.60 REMARK 200 R MERGE FOR SHELL (I) : 0.69720 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.810 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.88 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M SODIUM CITRATE TRIBASIC REMARK 280 DIHYDRATE, 20% W/V POLYETHYLENE GLYCOL 3,350, VAPOR DIFFUSION, REMARK 280 SITTING 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 39.90000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.75000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 39.90000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 22.75000 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 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 MET A 1 REMARK 465 GLY A 273 REMARK 465 VAL A 274 REMARK 465 ALA A 275 REMARK 465 GLU A 276 REMARK 465 GLU A 277 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 OD1 ASP A 14 NH1 ARG A 200 3445 1.72 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 ASN A 4 -146.33 -85.47 REMARK 500 THR A 6 -106.43 -130.93 REMARK 500 LEU A 49 69.42 -59.20 REMARK 500 SER A 79 94.99 -61.13 REMARK 500 THR A 138 97.48 -69.71 REMARK 500 ASP A 167 -88.06 -79.86 REMARK 500 ASP A 168 -134.79 -141.38 REMARK 500 LEU A 169 71.24 33.69 REMARK 500 ARG A 200 22.51 -69.69 REMARK 500 LEU A 203 -72.61 -69.98 REMARK 500 PHE A 235 129.34 179.29 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 324 DISTANCE = 8.02 ANGSTROMS REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6P7R RELATED DB: PDB DBREF 6P7T A 1 277 UNP Q9F5Q9 Q9F5Q9_VIBCL 1 277 SEQADV 6P7T ALA A 231 UNP Q9F5Q9 LYS 231 ENGINEERED MUTATION SEQRES 1 A 277 MET ARG GLU ASN ASN THR SER PHE LEU VAL ASN VAL TYR SEQRES 2 A 277 ASP LEU LYS LYS PHE ASP THR TYR ALA PHE ASN LYS VAL SEQRES 3 A 277 PHE ILE ASP ASP TYR LYS ILE PHE TRP ILE ASN LYS GLY SEQRES 4 A 277 SER ALA LYS LEU VAL ASP LYS ASN CYS LEU VAL SER TYR SEQRES 5 A 277 THR ILE THR ALA SER SER VAL VAL LEU LEU LYS LYS ASN SEQRES 6 A 277 SER ILE GLN ARG PHE SER LEU MET SER LEU SER ASP GLU SEQRES 7 A 277 SER ILE SER VAL CYS VAL LEU THR ILE LYS ASN LYS PHE SEQRES 8 A 277 VAL ASN SER LEU ARG HIS TYR LEU GLN GLY ASP LEU MET SEQRES 9 A 277 ILE ARG ASN LEU TYR ASN GLU LYS LYS ASP LEU LEU LEU SEQRES 10 A 277 TRP ASN CYS GLU LEU ASN ASP ILE SER VAL LEU GLY GLU SEQRES 11 A 277 ILE VAL SER THR TYR ASP GLN THR GLN TYR SER GLU ASP SEQRES 12 A 277 PHE LEU LYS ILE PHE PHE SER GLY PHE PHE SER LYS VAL SEQRES 13 A 277 GLU LYS LYS TYR ASN SER ILE PHE ILE THR ASP ASP LEU SEQRES 14 A 277 ASP ALA MET GLU LYS ILE SER CYS LEU VAL LYS SER ASP SEQRES 15 A 277 ILE THR ARG ASN TRP ARG TRP ALA ASP ILE CYS GLY GLU SEQRES 16 A 277 LEU ARG THR ASN ARG MET ILE LEU LYS LYS GLU LEU GLU SEQRES 17 A 277 SER ARG GLY VAL LYS PHE ARG GLU LEU ILE ASN SER ILE SEQRES 18 A 277 ARG ILE SER TYR SER ILE SER LEU MET ALA THR GLY GLU SEQRES 19 A 277 PHE LYS ILE LYS GLN ILE ALA TYR GLN SER GLY PHE ALA SEQRES 20 A 277 SER VAL SER TYR PHE SER THR VAL PHE LYS SER THR MET SEQRES 21 A 277 ASN VAL ALA PRO SER GLU TYR LEU PHE MET LEU THR GLY SEQRES 22 A 277 VAL ALA GLU GLU FORMUL 2 HOH *24(H2 O) HELIX 1 AA1 LYS A 88 LEU A 99 1 12 HELIX 2 AA2 ASN A 107 LYS A 113 1 7 HELIX 3 AA3 GLU A 121 SER A 133 1 13 HELIX 4 AA4 TYR A 140 ASN A 161 1 22 HELIX 5 AA5 ASP A 170 SER A 181 1 12 HELIX 6 AA6 ARG A 188 ARG A 197 1 10 HELIX 7 AA7 MET A 201 SER A 209 1 9 HELIX 8 AA8 LYS A 213 ALA A 231 1 19 HELIX 9 AA9 LYS A 236 SER A 244 1 9 HELIX 10 AB1 SER A 248 ASN A 261 1 14 HELIX 11 AB2 ALA A 263 THR A 272 1 10 SHEET 1 AA1 5 PHE A 8 LEU A 15 0 SHEET 2 AA1 5 ILE A 80 ILE A 87 -1 O ILE A 80 N LEU A 15 SHEET 3 AA1 5 TYR A 31 ILE A 36 -1 N TYR A 31 O ILE A 87 SHEET 4 AA1 5 SER A 58 LEU A 62 -1 O LEU A 62 N LYS A 32 SHEET 5 AA1 5 LEU A 115 ASN A 119 -1 O TRP A 118 N VAL A 59 SHEET 1 AA2 4 THR A 20 ILE A 28 0 SHEET 2 AA2 4 SER A 66 SER A 74 -1 O LEU A 72 N TYR A 21 SHEET 3 AA2 4 ALA A 41 ASP A 45 -1 N VAL A 44 O SER A 71 SHEET 4 AA2 4 VAL A 50 ILE A 54 -1 O TYR A 52 N LEU A 43 CISPEP 1 TYR A 135 ASP A 136 0 14.17 CRYST1 79.800 45.500 77.000 90.00 97.70 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 0.012531 0.000000 0.001694 0.00000 SCALE2 0.000000 0.021978 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013105 0.00000