HEADER UNKNOWN FUNCTION 17-MAY-18 6DGG TITLE CRONOBACTER TURICENSIS RPFR QUORUM-SENSING RECEPTOR PAS DOMAIN IN TITLE 2 COMPLEX WITH C12:0 COMPND MOL_ID: 1; COMPND 2 MOLECULE: RPFR; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PROTEIN GMR; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CRONOBACTER TURICENSIS (STRAIN DSM 18703 / LMG SOURCE 3 23827 / Z3032); SOURCE 4 ORGANISM_TAXID: 693216; SOURCE 5 STRAIN: DSM 18703 / LMG 23827 / Z3032; SOURCE 6 GENE: GMR, CTU_23300; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS QUORUM SENSING, DIFFUSIBLE SIGNAL FACTOR, DIGUANYLATE CYCLASE, KEYWDS 2 PHOSPHODIESTERASE, UNKNOWN FUNCTION EXPDTA X-RAY DIFFRACTION AUTHOR E.J.WALDRON,M.B.NEIDITCH REVDAT 5 11-OCT-23 6DGG 1 REMARK REVDAT 4 18-DEC-19 6DGG 1 REMARK REVDAT 3 27-MAR-19 6DGG 1 JRNL REVDAT 2 09-JAN-19 6DGG 1 REMARK REVDAT 1 02-JAN-19 6DGG 0 JRNL AUTH E.J.WALDRON,D.SNYDER,N.L.FERNANDEZ,E.SILEO,D.INOYAMA, JRNL AUTH 2 J.S.FREUNDLICH,C.M.WATERS,V.S.COOPER,M.B.NEIDITCH JRNL TITL STRUCTURAL BASIS OF DSF RECOGNITION BY ITS RECEPTOR RPFR AND JRNL TITL 2 ITS REGULATORY INTERACTION WITH THE DSF SYNTHASE RPFF. JRNL REF PLOS BIOL. V. 17 00123 2019 JRNL REFN ESSN 1545-7885 JRNL PMID 30716063 JRNL DOI 10.1371/JOURNAL.PBIO.3000123 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.12_2829 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.52 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.2 REMARK 3 NUMBER OF REFLECTIONS : 13221 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.150 REMARK 3 R VALUE (WORKING SET) : 0.147 REMARK 3 FREE R VALUE : 0.174 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.940 REMARK 3 FREE R VALUE TEST SET COUNT : 1314 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 37.5292 - 3.1156 0.98 1421 159 0.1465 0.1517 REMARK 3 2 3.1156 - 2.4731 0.98 1394 157 0.1439 0.1632 REMARK 3 3 2.4731 - 2.1605 0.96 1347 144 0.1283 0.1823 REMARK 3 4 2.1605 - 1.9630 0.98 1364 149 0.1308 0.1517 REMARK 3 5 1.9630 - 1.8223 0.98 1364 153 0.1441 0.1695 REMARK 3 6 1.8223 - 1.7148 0.93 1300 142 0.1594 0.2195 REMARK 3 7 1.7148 - 1.6290 0.92 1287 142 0.1668 0.2178 REMARK 3 8 1.6290 - 1.5580 0.91 1267 134 0.1792 0.2234 REMARK 3 9 1.5580 - 1.4981 0.85 1163 134 0.1846 0.2351 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) : 0.120 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.790 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 9.32 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.46 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 : 0.005 872 REMARK 3 ANGLE : 0.893 1168 REMARK 3 CHIRALITY : 0.077 127 REMARK 3 PLANARITY : 0.005 151 REMARK 3 DIHEDRAL : 23.540 330 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 5 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 123 THROUGH 162 ) REMARK 3 ORIGIN FOR THE GROUP (A): 3.9833 4.5883 8.4479 REMARK 3 T TENSOR REMARK 3 T11: 0.0866 T22: 0.0353 REMARK 3 T33: 0.0550 T12: -0.0104 REMARK 3 T13: -0.0103 T23: -0.0001 REMARK 3 L TENSOR REMARK 3 L11: 2.3842 L22: 2.7212 REMARK 3 L33: 2.1743 L12: -0.4575 REMARK 3 L13: 0.0641 L23: 0.2101 REMARK 3 S TENSOR REMARK 3 S11: -0.0248 S12: 0.0819 S13: -0.0407 REMARK 3 S21: -0.0914 S22: 0.0417 S23: 0.0974 REMARK 3 S31: 0.1740 S32: -0.0412 S33: -0.0171 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 163 THROUGH 179 ) REMARK 3 ORIGIN FOR THE GROUP (A): 15.8703 12.2905 0.6806 REMARK 3 T TENSOR REMARK 3 T11: 0.1158 T22: 0.0724 REMARK 3 T33: 0.0808 T12: -0.0105 REMARK 3 T13: 0.0239 T23: 0.0003 REMARK 3 L TENSOR REMARK 3 L11: 7.8009 L22: 7.7604 REMARK 3 L33: 1.7976 L12: -7.1990 REMARK 3 L13: -0.9729 L23: -0.3129 REMARK 3 S TENSOR REMARK 3 S11: 0.2228 S12: 0.1858 S13: 0.3218 REMARK 3 S21: -0.3443 S22: -0.2020 S23: -0.3525 REMARK 3 S31: 0.1259 S32: 0.1213 S33: -0.0228 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 180 THROUGH 193 ) REMARK 3 ORIGIN FOR THE GROUP (A): 8.7615 15.6679 10.3837 REMARK 3 T TENSOR REMARK 3 T11: 0.1115 T22: 0.0364 REMARK 3 T33: 0.0228 T12: 0.0045 REMARK 3 T13: 0.0135 T23: -0.0145 REMARK 3 L TENSOR REMARK 3 L11: 3.3721 L22: 3.8196 REMARK 3 L33: 2.4208 L12: 0.3667 REMARK 3 L13: 1.9133 L23: -0.5898 REMARK 3 S TENSOR REMARK 3 S11: -0.0166 S12: 0.1346 S13: 0.0522 REMARK 3 S21: -0.1258 S22: 0.0475 S23: 0.1707 REMARK 3 S31: -0.0429 S32: 0.0373 S33: -0.0151 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 194 THROUGH 224 ) REMARK 3 ORIGIN FOR THE GROUP (A): 12.2407 10.2304 12.9788 REMARK 3 T TENSOR REMARK 3 T11: 0.0849 T22: 0.0327 REMARK 3 T33: 0.0255 T12: -0.0113 REMARK 3 T13: 0.0104 T23: 0.0049 REMARK 3 L TENSOR REMARK 3 L11: 2.8838 L22: 4.1099 REMARK 3 L33: 2.4251 L12: -1.1323 REMARK 3 L13: -0.5473 L23: 1.0990 REMARK 3 S TENSOR REMARK 3 S11: -0.0151 S12: 0.0790 S13: -0.1329 REMARK 3 S21: 0.0269 S22: 0.0092 S23: -0.0117 REMARK 3 S31: 0.1627 S32: 0.0474 S33: 0.0038 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 116 THROUGH 122 ) REMARK 3 ORIGIN FOR THE GROUP (A): 2.5437 5.3155 26.6541 REMARK 3 T TENSOR REMARK 3 T11: 0.2124 T22: 0.1276 REMARK 3 T33: 0.2150 T12: 0.0517 REMARK 3 T13: 0.0835 T23: 0.0739 REMARK 3 L TENSOR REMARK 3 L11: 8.7461 L22: 5.1208 REMARK 3 L33: 8.2021 L12: 6.6540 REMARK 3 L13: -7.6881 L23: -6.1152 REMARK 3 S TENSOR REMARK 3 S11: -0.0614 S12: -0.3261 S13: -0.3106 REMARK 3 S21: 0.4812 S22: 0.1935 S23: 0.4291 REMARK 3 S31: -0.1489 S32: -0.0855 S33: -0.0691 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 6DGG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-MAY-18. REMARK 100 THE DEPOSITION ID IS D_1000234564. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-DEC-16 REMARK 200 TEMPERATURE (KELVIN) : 93 REMARK 200 PH : 7.75 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL9-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.88557 REMARK 200 MONOCHROMATOR : SI(111) AND SI(220) DOUBLE REMARK 200 CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13614 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.498 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 200 DATA REDUNDANCY : 3.200 REMARK 200 R MERGE (I) : 0.06500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.0900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.3 REMARK 200 DATA REDUNDANCY IN SHELL : 2.70 REMARK 200 R MERGE FOR SHELL (I) : 0.22100 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: PHASER REMARK 200 STARTING MODEL: 5IU1 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 28.49 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.72 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 200 MM SODIUM FORMATE, 18% (VOL/VOL) REMARK 280 PEG 3350, 100 MM HEPES (PH 7.75), 1MM BDSF AND 0.62% (VOL/VOL) REMARK 280 DMSO, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 14.56550 REMARK 290 SMTRY3 2 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 GLN A 115 REMARK 465 SER A 207 REMARK 465 GLY A 208 REMARK 465 SER A 209 REMARK 465 GLY A 210 REMARK 465 ARG A 211 REMARK 465 ASN A 212 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 179 28.36 -151.91 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 DAO A 301 DBREF 6DGG A 115 224 UNP C9XTL5 C9XTL5_CROTZ 135 244 SEQRES 1 A 110 GLN VAL VAL SER GLU ALA ASN SER VAL ILE VAL ILE LEU SEQRES 2 A 110 ASP ARG HIS GLY ASN ILE GLN ARG PHE ASN ARG LEU SER SEQRES 3 A 110 GLU GLU TYR THR GLY LEU LYS GLU GLN GLU VAL ILE GLY SEQRES 4 A 110 GLN ASN VAL PHE THR LEU PHE MET SER PRO ALA GLU ALA SEQRES 5 A 110 SER ALA SER ARG ARG ASN VAL THR GLY PHE PHE ARG ASN SEQRES 6 A 110 GLY SER SER TYR GLU VAL GLU ARG TRP ILE LYS THR ARG SEQRES 7 A 110 LYS GLY GLN ARG LEU PHE LEU PHE ARG ASN LYS PHE VAL SEQRES 8 A 110 HIS SER GLY SER GLY ARG ASN GLU ILE PHE LEU ILE CYS SEQRES 9 A 110 SER GLY THR ASP ILE THR HET DAO A 301 37 HETNAM DAO LAURIC ACID FORMUL 2 DAO C12 H24 O2 FORMUL 3 HOH *89(H2 O) HELIX 1 AA1 ASN A 137 GLY A 145 1 9 HELIX 2 AA2 LYS A 147 ILE A 152 1 6 HELIX 3 AA3 ASN A 155 MET A 161 1 7 HELIX 4 AA4 SER A 162 GLY A 180 1 19 SHEET 1 AA1 5 ILE A 133 PHE A 136 0 SHEET 2 AA1 5 VAL A 123 LEU A 127 -1 N ILE A 126 O GLN A 134 SHEET 3 AA1 5 LEU A 216 ASP A 222 -1 O GLY A 220 N VAL A 123 SHEET 4 AA1 5 GLY A 194 PHE A 204 -1 N LYS A 203 O ILE A 217 SHEET 5 AA1 5 TYR A 183 THR A 191 -1 N VAL A 185 O PHE A 200 SITE 1 AC1 8 VAL A 156 SER A 169 ASN A 172 TYR A 183 SITE 2 AC1 8 VAL A 185 ARG A 187 PHE A 200 ASN A 202 CRYST1 39.682 29.131 41.493 90.00 115.29 90.00 P 1 21 1 2 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 0.025200 0.000000 0.011905 0.00000 SCALE2 0.000000 0.034328 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026654 0.00000