HEADER TRANSCRIPTION/TRANSCRIPTION INHIBITOR 04-AUG-16 5SUX TITLE CRYSTAL STRUCTURE OF TOXT FROM VIBRIO CHOLERAE O395 BOUND TO (E)-4-(8- TITLE 2 METHYLNAPHTHALEN-1-YL)BUT-3-ENOIC ACID COMPND MOL_ID: 1; COMPND 2 MOLECULE: ARAC FAMILY TRANSCRIPTIONAL REGULATOR; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: TCP PILUS VIRULENCE REGULATORY PROTEIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VIBRIO CHOLERAE; SOURCE 3 ORGANISM_TAXID: 666; SOURCE 4 GENE: TOXT, TCPN, EN12_04130, ERS013198_02000, ERS013199_00625, SOURCE 5 ERS013200_01425, ERS013202_00629, ERS013206_00617, ERS013207_01424; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TRANSCRIPTIONAL ACTIVATOR, PROTEIN-INHIBITOR COMPLEX, TRANSCRIPTION- KEYWDS 2 TRANSCRIPTION INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR F.J.KULL,A.R.KELLEY REVDAT 4 11-DEC-19 5SUX 1 REMARK REVDAT 3 20-SEP-17 5SUX 1 REMARK REVDAT 2 09-AUG-17 5SUX 1 REMARK REVDAT 1 12-APR-17 5SUX 0 JRNL AUTH F.J.KULL,A.R.KELLEY JRNL TITL CRYSTAL STRUCTURE OF TOXT FROM VIBRIO CHOLERAE O395 BOUND TO JRNL TITL 2 (E)-4-(8-METHYLNAPHTHALEN-1-YL)BUT-3-ENOIC ACID JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10.1_2155) 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.25 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 36076 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.191 REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : 0.230 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.090 REMARK 3 FREE R VALUE TEST SET COUNT : 1835 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 42.2544 - 4.7010 0.99 2628 139 0.1710 0.1917 REMARK 3 2 4.7010 - 3.7320 0.98 2595 148 0.1454 0.1759 REMARK 3 3 3.7320 - 3.2605 0.99 2626 128 0.1673 0.2347 REMARK 3 4 3.2605 - 2.9625 0.99 2630 144 0.1818 0.2364 REMARK 3 5 2.9625 - 2.7502 1.00 2645 137 0.1918 0.2675 REMARK 3 6 2.7502 - 2.5880 1.00 2630 149 0.1905 0.2305 REMARK 3 7 2.5880 - 2.4584 1.00 2636 152 0.2069 0.2607 REMARK 3 8 2.4584 - 2.3514 1.00 2653 124 0.2094 0.2324 REMARK 3 9 2.3514 - 2.2609 1.00 2644 148 0.2230 0.2636 REMARK 3 10 2.2609 - 2.1829 1.00 2685 147 0.2350 0.2723 REMARK 3 11 2.1829 - 2.1147 1.00 2634 132 0.2601 0.2973 REMARK 3 12 2.1147 - 2.0542 1.00 2614 155 0.2791 0.3563 REMARK 3 13 2.0542 - 2.0001 1.00 2621 132 0.3289 0.3510 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) : 0.230 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.060 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.003 2274 REMARK 3 ANGLE : 0.611 3058 REMARK 3 CHIRALITY : 0.044 340 REMARK 3 PLANARITY : 0.002 373 REMARK 3 DIHEDRAL : 15.072 1358 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 7.8967 -14.2580 -21.2521 REMARK 3 T TENSOR REMARK 3 T11: 0.1470 T22: 0.1534 REMARK 3 T33: 0.1657 T12: -0.0018 REMARK 3 T13: 0.0027 T23: -0.0019 REMARK 3 L TENSOR REMARK 3 L11: 0.4494 L22: 0.7047 REMARK 3 L33: 0.9235 L12: 0.1997 REMARK 3 L13: -0.0630 L23: -0.2549 REMARK 3 S TENSOR REMARK 3 S11: -0.0177 S12: 0.0395 S13: -0.0514 REMARK 3 S21: -0.0775 S22: 0.0043 S23: 0.0262 REMARK 3 S31: 0.0762 S32: -0.0326 S33: -0.0001 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 5SUX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-AUG-16. REMARK 100 THE DEPOSITION ID IS D_1000223185. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-MAR-16 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 : APS REMARK 200 BEAMLINE : 23-ID-B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.033 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 2564 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 42.250 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 4.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.9100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL 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: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.03 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50% PROTEIN BUFFER: 20 MM TRIS, 1 MM REMARK 280 EDTA, 320 MM NACL, PH 7.5 50% RESERVOIR SOLUTION: 0.1 M MES PH REMARK 280 6.5 AND 15% (W/V) PEG 400, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 20.26000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 42.24500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 40.48000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 42.24500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.26000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 40.48000 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 ILE A 2 REMARK 465 GLY A 3 REMARK 465 LYS A 4 REMARK 465 GLY A 272 REMARK 465 VAL A 273 REMARK 465 ALA A 274 REMARK 465 GLU A 275 REMARK 465 LYS A 276 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 PHE A 17 20.00 55.94 REMARK 500 LEU A 99 -13.75 70.76 REMARK 500 GLU A 110 26.81 -145.00 REMARK 500 GLU A 136 -87.35 -122.55 REMARK 500 ASP A 181 72.60 -154.33 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 70H A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MES A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MES A 303 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3GBG RELATED DB: PDB REMARK 900 3GBG CONTAINS THE SAME PROTEIN COMPLEXED WITH THE LIGAND PAM. REMARK 900 RELATED ID: 5SUW RELATED DB: PDB DBREF 5SUX A 1 276 UNP Q7BGC0 Q7BGC0_VIBCL 1 276 SEQRES 1 A 276 MET ILE GLY LYS LYS SER PHE GLN THR ASN VAL TYR ARG SEQRES 2 A 276 MET SER LYS PHE ASP THR TYR ILE PHE ASN ASN LEU TYR SEQRES 3 A 276 ILE ASN ASP TYR LYS MET PHE TRP ILE ASP SER GLY ILE SEQRES 4 A 276 ALA LYS LEU ILE ASP LYS ASN CYS LEU VAL SER TYR GLU SEQRES 5 A 276 ILE ASN SER SER SER ILE ILE LEU LEU LYS LYS ASN SER SEQRES 6 A 276 ILE GLN ARG PHE SER LEU THR SER LEU SER ASP GLU ASN SEQRES 7 A 276 ILE ASN VAL SER VAL ILE THR ILE SER ASP SER PHE ILE SEQRES 8 A 276 ARG SER LEU LYS SER TYR ILE LEU GLY ASP LEU MET ILE SEQRES 9 A 276 ARG ASN LEU TYR SER GLU ASN LYS ASP LEU LEU LEU TRP SEQRES 10 A 276 ASN CYS GLU HIS ASN ASP ILE ALA VAL LEU SER GLU VAL SEQRES 11 A 276 VAL ASN GLY PHE ARG GLU ILE ASN TYR SER ASP GLU PHE SEQRES 12 A 276 LEU LYS VAL PHE PHE SER GLY PHE PHE SER LYS VAL GLU SEQRES 13 A 276 LYS LYS TYR ASN SER ILE PHE ILE THR ASP ASP LEU ASP SEQRES 14 A 276 ALA MET GLU LYS ILE SER CYS LEU VAL LYS SER ASP ILE SEQRES 15 A 276 THR ARG ASN TRP ARG TRP ALA ASP ILE CYS GLY GLU LEU SEQRES 16 A 276 ARG THR ASN ARG MET ILE LEU LYS LYS GLU LEU GLU SER SEQRES 17 A 276 ARG GLY VAL LYS PHE ARG GLU LEU ILE ASN SER ILE ARG SEQRES 18 A 276 ILE SER TYR SER ILE SER LEU MET LYS THR GLY GLU PHE SEQRES 19 A 276 LYS ILE LYS GLN ILE ALA TYR GLN SER GLY PHE ALA SER SEQRES 20 A 276 VAL SER TYR PHE SER THR VAL PHE LYS SER THR MET ASN SEQRES 21 A 276 VAL ALA PRO SER GLU TYR LEU PHE MET LEU THR GLY VAL SEQRES 22 A 276 ALA GLU LYS HET 70H A 301 17 HET MES A 302 12 HET MES A 303 12 HETNAM 70H (3E)-4-(8-METHYLNAPHTHALEN-1-YL)BUT-3-ENOIC ACID HETNAM MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID FORMUL 2 70H C15 H14 O2 FORMUL 3 MES 2(C6 H13 N O4 S) FORMUL 5 HOH *79(H2 O) HELIX 1 AA1 SER A 87 SER A 93 1 7 HELIX 2 AA2 ASP A 101 ASN A 106 1 6 HELIX 3 AA3 GLU A 120 ASN A 132 1 13 HELIX 4 AA4 SER A 140 ASN A 160 1 21 HELIX 5 AA5 ASP A 169 SER A 180 1 12 HELIX 6 AA6 ARG A 187 ARG A 196 1 10 HELIX 7 AA7 ASN A 198 SER A 208 1 11 HELIX 8 AA8 LYS A 212 THR A 231 1 20 HELIX 9 AA9 LYS A 235 SER A 243 1 9 HELIX 10 AB1 SER A 247 ASN A 260 1 14 HELIX 11 AB2 ALA A 262 LEU A 270 1 9 SHEET 1 AA1 5 PHE A 7 MET A 14 0 SHEET 2 AA1 5 ILE A 79 ILE A 86 -1 O THR A 85 N GLN A 8 SHEET 3 AA1 5 LYS A 31 ILE A 35 -1 N MET A 32 O ILE A 84 SHEET 4 AA1 5 SER A 57 LEU A 61 -1 O LEU A 61 N LYS A 31 SHEET 5 AA1 5 LEU A 114 ASN A 118 -1 O TRP A 117 N ILE A 58 SHEET 1 AA2 4 THR A 19 TYR A 26 0 SHEET 2 AA2 4 ILE A 66 SER A 73 -1 O PHE A 69 N PHE A 22 SHEET 3 AA2 4 ALA A 40 ASP A 44 -1 N LYS A 41 O THR A 72 SHEET 4 AA2 4 VAL A 49 ILE A 53 -1 O TYR A 51 N LEU A 42 SITE 1 AC1 7 TYR A 12 PHE A 22 LYS A 31 PHE A 33 SITE 2 AC1 7 LYS A 230 TYR A 266 HOH A 401 SITE 1 AC2 8 ASN A 28 LYS A 179 TYR A 224 SER A 227 SITE 2 AC2 8 LEU A 228 THR A 231 HOH A 402 HOH A 418 SITE 1 AC3 5 TRP A 117 ASN A 118 ILE A 137 LYS A 158 SITE 2 AC3 5 HOH A 410 CRYST1 40.520 80.960 84.490 90.00 90.00 90.00 P 21 21 21 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 0.024679 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012352 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011836 0.00000 MASTER 274 0 3 11 9 0 6 6 0 0 0 22 END