HEADER UNKNOWN FUNCTION 17-MAY-18 6DGJ TITLE CRONOBACTER TURICENSIS RPFR QUORUM-SENSING RECEPTOR PAS DOMAIN IN TITLE 2 COMPLEX WITH BDSF 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 4 13-MAR-24 6DGJ 1 REMARK REVDAT 3 18-DEC-19 6DGJ 1 REMARK REVDAT 2 27-MAR-19 6DGJ 1 JRNL REVDAT 1 02-JAN-19 6DGJ 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. 2.29 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) : 2.29 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.51 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 3998 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.233 REMARK 3 R VALUE (WORKING SET) : 0.228 REMARK 3 FREE R VALUE : 0.282 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.950 REMARK 3 FREE R VALUE TEST SET COUNT : 398 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 37.5141 - 3.3074 1.00 1228 138 0.1947 0.2505 REMARK 3 2 3.3074 - 2.6254 1.00 1194 134 0.2433 0.2835 REMARK 3 3 2.6254 - 2.2936 0.99 1178 126 0.2820 0.3651 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) : 0.380 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 31.050 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.90 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 : 0.003 857 REMARK 3 ANGLE : 0.522 1146 REMARK 3 CHIRALITY : 0.042 125 REMARK 3 PLANARITY : 0.002 149 REMARK 3 DIHEDRAL : 17.681 512 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 116 THROUGH 151 ) REMARK 3 ORIGIN FOR THE GROUP (A): 3.8364 18.2766 13.2246 REMARK 3 T TENSOR REMARK 3 T11: 0.2027 T22: 0.1156 REMARK 3 T33: 0.1361 T12: 0.0015 REMARK 3 T13: -0.0210 T23: 0.0012 REMARK 3 L TENSOR REMARK 3 L11: 3.4779 L22: 2.2991 REMARK 3 L33: 2.2483 L12: 0.2928 REMARK 3 L13: 0.2906 L23: -1.0944 REMARK 3 S TENSOR REMARK 3 S11: 0.0705 S12: -0.1507 S13: -0.1324 REMARK 3 S21: 0.3537 S22: 0.1980 S23: 0.0874 REMARK 3 S31: 0.2489 S32: -0.0827 S33: -0.2121 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 152 THROUGH 176 ) REMARK 3 ORIGIN FOR THE GROUP (A): 9.1943 25.7398 1.5726 REMARK 3 T TENSOR REMARK 3 T11: 0.2631 T22: 0.1973 REMARK 3 T33: 0.1428 T12: -0.0133 REMARK 3 T13: 0.0311 T23: -0.0250 REMARK 3 L TENSOR REMARK 3 L11: 1.6380 L22: 3.1924 REMARK 3 L33: 1.6142 L12: -1.9671 REMARK 3 L13: 1.3715 L23: -1.0451 REMARK 3 S TENSOR REMARK 3 S11: -0.0284 S12: 0.4252 S13: -0.0209 REMARK 3 S21: 0.0833 S22: -0.2022 S23: 0.0139 REMARK 3 S31: -0.0324 S32: 0.0737 S33: 0.2408 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 177 THROUGH 224 ) REMARK 3 ORIGIN FOR THE GROUP (A): 11.7617 26.7699 10.9350 REMARK 3 T TENSOR REMARK 3 T11: 0.1914 T22: 0.0901 REMARK 3 T33: 0.1175 T12: -0.0289 REMARK 3 T13: -0.0455 T23: -0.0225 REMARK 3 L TENSOR REMARK 3 L11: 1.7275 L22: 3.9852 REMARK 3 L33: 2.8136 L12: -1.1004 REMARK 3 L13: -0.8325 L23: 0.5559 REMARK 3 S TENSOR REMARK 3 S11: 0.1749 S12: 0.0763 S13: -0.0498 REMARK 3 S21: -0.2515 S22: -0.0581 S23: 0.0250 REMARK 3 S31: -0.1998 S32: 0.1248 S33: -0.1094 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 6DGJ 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_1000234577. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-SEP-17 REMARK 200 TEMPERATURE (KELVIN) : 93 REMARK 200 PH : NULL 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 MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54178 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4004 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.294 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 (%) : 99.9 REMARK 200 DATA REDUNDANCY : 3.900 REMARK 200 R MERGE (I) : 0.20600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.3300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.29 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.34 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : 0.61800 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 28.97 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.73 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 150 MM LITHIUM CITRATE AND 16% REMARK 280 (VOL/VOL) PEG 3350, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 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 14.57500 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 HIS A 206 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: 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 HE21 GLN A 149 O GLN A 195 1545 1.59 REMARK 500 NE2 GLN A 149 O GLN A 195 1545 2.13 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 LYS A 193 50.13 -114.41 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 GEY A 301 DBREF 6DGJ 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 GEY A 301 35 HETNAM GEY (2Z)-DODEC-2-ENOIC ACID FORMUL 2 GEY C12 H22 O2 FORMUL 3 HOH *38(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 PHE A 177 1 16 SHEET 1 AA1 5 ILE A 133 PHE A 136 0 SHEET 2 AA1 5 VAL A 123 ASP A 128 -1 N ILE A 126 O GLN A 134 SHEET 3 AA1 5 PHE A 215 ASP A 222 -1 O LEU A 216 N LEU A 127 SHEET 4 AA1 5 GLY A 194 PHE A 204 -1 N ARG A 201 O SER A 219 SHEET 5 AA1 5 TYR A 183 THR A 191 -1 N ILE A 189 O ARG A 196 SITE 1 AC1 12 THR A 144 VAL A 156 PHE A 160 SER A 169 SITE 2 AC1 12 ASN A 172 VAL A 173 TYR A 183 VAL A 185 SITE 3 AC1 12 ARG A 187 ILE A 189 ASN A 202 CYS A 218 CRYST1 39.932 29.150 41.554 90.00 115.49 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 0.025043 0.000000 0.011939 0.00000 SCALE2 0.000000 0.034305 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026660 0.00000