HEADER DNA BINDING PROTEIN 29-OCT-19 6UTC TITLE INTRA-CHAIN DISULFIDE BONDED TOXR PERIPLASMIC DOMAIN FROM VIBRIO TITLE 2 VULNIFICUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSCRIPTIONAL ACTIVATOR TOXR; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: PERIPLASMIC DOMAIN; COMPND 5 SYNONYM: TRANSCRIPTIONAL REGULATOR,TRANSMEMBRANE TRANSCRIPTION COMPND 6 ACTIVATOR; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VIBRIO VULNIFICUS; SOURCE 3 ORGANISM_TAXID: 672; SOURCE 4 GENE: TOXR, CRN46_04050, D8T65_08455, FORC36_0761; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: SHUFFLE T7 EXPRESS; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET-VVTOXRP KEYWDS SENSOR, PERIPLASM, TOXR, ALPHA-BETA, DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR C.R.MIDGETT,R.A.SWINDELL,F.J.KULL REVDAT 2 03-APR-24 6UTC 1 REMARK REVDAT 1 17-JUN-20 6UTC 0 JRNL AUTH C.R.MIDGETT,R.A.SWINDELL,M.PELLEGRINI,F.JON KULL JRNL TITL A DISULFIDE CONSTRAINS THE TOXR PERIPLASMIC DOMAIN JRNL TITL 2 STRUCTURE, ALTERING ITS INTERACTIONS WITH TOXS AND JRNL TITL 3 BILE-SALTS. JRNL REF SCI REP V. 10 9002 2020 JRNL REFN ESSN 2045-2322 JRNL PMID 32488093 JRNL DOI 10.1038/S41598-020-66050-5 REMARK 2 REMARK 2 RESOLUTION. 1.25 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.15_3459 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) : 1.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.43 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 87.3 REMARK 3 NUMBER OF REFLECTIONS : 20411 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.194 REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : 0.213 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.830 REMARK 3 FREE R VALUE TEST SET COUNT : 3748 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 28.4280 - 3.7446 1.00 1451 160 0.1625 0.1668 REMARK 3 2 3.7446 - 2.9732 1.00 1476 155 0.1762 0.2106 REMARK 3 3 2.9732 - 2.5977 1.00 1462 157 0.1868 0.2051 REMARK 3 4 2.5977 - 2.3603 1.00 1451 149 0.1908 0.2470 REMARK 3 5 2.3603 - 2.1912 1.00 1464 158 0.1820 0.1850 REMARK 3 6 2.1912 - 2.0620 1.00 1451 169 0.1866 0.1920 REMARK 3 7 2.0620 - 1.9588 1.00 1436 154 0.1968 0.2135 REMARK 3 8 1.9588 - 1.8735 0.99 1461 155 0.1937 0.2224 REMARK 3 9 1.8735 - 1.8014 0.99 1447 153 0.1937 0.2226 REMARK 3 10 1.8014 - 1.7393 0.99 1436 158 0.2062 0.1977 REMARK 3 11 1.7393 - 1.6849 1.00 1447 152 0.1966 0.2069 REMARK 3 12 1.6849 - 1.6367 0.99 1481 156 0.2035 0.2389 REMARK 3 13 1.6367 - 1.5936 0.98 1418 155 0.1965 0.2298 REMARK 3 14 1.5936 - 1.5548 1.00 1454 160 0.2109 0.2469 REMARK 3 15 1.5548 - 1.5194 0.97 1399 168 0.2136 0.2154 REMARK 3 16 1.5194 - 1.4871 0.98 1415 147 0.2061 0.2118 REMARK 3 17 1.4871 - 1.4573 0.97 1428 160 0.2175 0.2891 REMARK 3 18 1.4573 - 1.4298 0.96 1371 150 0.2254 0.2562 REMARK 3 19 1.4298 - 1.4043 0.93 1374 153 0.2592 0.2921 REMARK 3 20 1.4043 - 1.3805 0.84 1222 140 0.2847 0.3394 REMARK 3 21 1.3805 - 1.3582 0.76 1096 117 0.2913 0.2811 REMARK 3 22 1.3582 - 1.3373 0.68 992 116 0.3348 0.2703 REMARK 3 23 1.3373 - 1.3177 0.61 900 91 0.3298 0.3366 REMARK 3 24 1.3177 - 1.2991 0.58 828 96 0.3378 0.4197 REMARK 3 25 1.2991 - 1.2816 0.52 768 79 0.3414 0.4264 REMARK 3 26 1.2816 - 1.2649 0.46 640 85 0.3701 0.3966 REMARK 3 27 1.2649 - 1.2491 0.42 630 55 0.4265 0.4520 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) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.810 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.79 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 6UTC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-OCT-19. REMARK 100 THE DEPOSITION ID IS D_1000245171. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-MAR-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.3 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) : 0.97933 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 : 20411 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.249 REMARK 200 RESOLUTION RANGE LOW (A) : 28.430 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 87.8 REMARK 200 DATA REDUNDANCY : 11.20 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 23.8400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.29 REMARK 200 COMPLETENESS FOR SHELL (%) : 47.1 REMARK 200 DATA REDUNDANCY IN SHELL : 5.30 REMARK 200 R MERGE FOR SHELL (I) : 0.91870 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.300 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: SE-MET-VVTOXRP REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 29.48 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.74 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 4 MG/ML VVTOXRP, 2.0 M AMMONIUM REMARK 280 SULFATE, 0.1 M NA CACODYLATE PH 6.3, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 298K 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 19.98500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 25.14000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 20.22000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 25.14000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.98500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 20.22000 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 187 REMARK 465 ALA A 188 REMARK 465 HIS A 189 REMARK 465 HIS A 190 REMARK 465 HIS A 191 REMARK 465 HIS A 192 REMARK 465 HIS A 193 REMARK 465 HIS A 194 REMARK 465 THR A 195 REMARK 465 ASN A 196 REMARK 465 PRO A 197 REMARK 465 SER A 198 REMARK 465 GLU A 199 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 GLU A 206 145.07 -173.66 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 SO4 A 301 DBREF 6UTC A 195 290 UNP Q9RP86 Q9RP86_VIBVL 195 290 SEQADV 6UTC MET A 187 UNP Q9RP86 INITIATING METHIONINE SEQADV 6UTC ALA A 188 UNP Q9RP86 EXPRESSION TAG SEQADV 6UTC HIS A 189 UNP Q9RP86 EXPRESSION TAG SEQADV 6UTC HIS A 190 UNP Q9RP86 EXPRESSION TAG SEQADV 6UTC HIS A 191 UNP Q9RP86 EXPRESSION TAG SEQADV 6UTC HIS A 192 UNP Q9RP86 EXPRESSION TAG SEQADV 6UTC HIS A 193 UNP Q9RP86 EXPRESSION TAG SEQADV 6UTC HIS A 194 UNP Q9RP86 EXPRESSION TAG SEQRES 1 A 104 MET ALA HIS HIS HIS HIS HIS HIS THR ASN PRO SER GLU SEQRES 2 A 104 SER LYS PHE ARG LEU LEU GLU ASN VAL ASN GLY VAL GLU SEQRES 3 A 104 VAL LEU THR PRO LEU ASN HIS PRO PRO LEU GLN ALA TRP SEQRES 4 A 104 MET PRO SER ILE ARG GLN CYS VAL ASN LYS TYR ALA GLU SEQRES 5 A 104 THR HIS THR GLY ASP SER ALA PRO VAL LYS VAL ILE ALA SEQRES 6 A 104 THR GLY GLY GLN GLY ASN GLN LEU ILE LEU ASN TYR ILE SEQRES 7 A 104 HIS THR LEU PRO HIS SER ASN GLU ASN VAL THR LEU ARG SEQRES 8 A 104 ILE PHE SER GLU GLN ASN ASP LEU GLY SER ILE CYS LYS HET SO4 A 301 5 HETNAM SO4 SULFATE ION FORMUL 2 SO4 O4 S 2- FORMUL 3 HOH *104(H2 O) HELIX 1 AA1 LEU A 222 ALA A 224 5 3 HELIX 2 AA2 TRP A 225 THR A 239 1 15 HELIX 3 AA3 HIS A 240 ALA A 245 5 6 HELIX 4 AA4 THR A 266 ASN A 273 5 8 HELIX 5 AA5 ASP A 284 CYS A 289 1 6 SHEET 1 AA1 5 PHE A 202 VAL A 208 0 SHEET 2 AA1 5 VAL A 211 PRO A 216 -1 O VAL A 213 N GLU A 206 SHEET 3 AA1 5 LYS A 248 GLY A 253 1 O ALA A 251 N LEU A 214 SHEET 4 AA1 5 GLN A 258 ILE A 264 -1 O ILE A 260 N THR A 252 SHEET 5 AA1 5 VAL A 274 PHE A 279 -1 O LEU A 276 N LEU A 261 SSBOND 1 CYS A 232 CYS A 289 1555 1555 2.05 SITE 1 AC1 10 ARG A 203 LEU A 205 PRO A 221 LEU A 222 SITE 2 AC1 10 GLN A 223 GLN A 231 LYS A 235 HOH A 406 SITE 3 AC1 10 HOH A 420 HOH A 437 CRYST1 39.970 40.440 50.280 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 0.025019 0.000000 0.000000 0.00000 SCALE2 0.000000 0.024728 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019889 0.00000