HEADER UNKNOWN FUNCTION 17-MAY-18 6DGA TITLE CRONOBACTER TURICENSIS RPFR QUORUM-SENSING RECEPTOR RPFF INTERACTION TITLE 2 DOMAIN 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 13-MAR-24 6DGA 1 REMARK REVDAT 4 18-DEC-19 6DGA 1 REMARK REVDAT 3 27-MAR-19 6DGA 1 JRNL REVDAT 2 16-JAN-19 6DGA 1 JRNL REVDAT 1 02-JAN-19 6DGA 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. 1.19 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.19 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.20 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.6 REMARK 3 NUMBER OF REFLECTIONS : 26536 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.164 REMARK 3 R VALUE (WORKING SET) : 0.161 REMARK 3 FREE R VALUE : 0.193 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.590 REMARK 3 FREE R VALUE TEST SET COUNT : 2015 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 28.2049 - 2.8679 0.95 1867 158 0.1761 0.1945 REMARK 3 2 2.8679 - 2.2767 1.00 1855 150 0.1657 0.1903 REMARK 3 3 2.2767 - 1.9890 0.99 1819 148 0.1482 0.1842 REMARK 3 4 1.9890 - 1.8071 0.99 1822 146 0.1534 0.1994 REMARK 3 5 1.8071 - 1.6776 0.99 1767 144 0.1457 0.1794 REMARK 3 6 1.6776 - 1.5787 0.98 1778 145 0.1371 0.1744 REMARK 3 7 1.5787 - 1.4997 0.97 1752 141 0.1376 0.1727 REMARK 3 8 1.4997 - 1.4344 0.97 1723 151 0.1435 0.2011 REMARK 3 9 1.4344 - 1.3792 0.97 1745 135 0.1473 0.2158 REMARK 3 10 1.3792 - 1.3316 0.96 1721 144 0.1582 0.2177 REMARK 3 11 1.3316 - 1.2900 0.96 1677 137 0.1667 0.2202 REMARK 3 12 1.2900 - 1.2531 0.95 1720 138 0.1685 0.2020 REMARK 3 13 1.2531 - 1.2201 0.95 1654 145 0.1839 0.2197 REMARK 3 14 1.2201 - 1.1903 0.90 1621 133 0.2333 0.2629 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 20.800 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.92 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.07 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 : 0.006 752 REMARK 3 ANGLE : 0.865 1029 REMARK 3 CHIRALITY : 0.074 125 REMARK 3 PLANARITY : 0.006 130 REMARK 3 DIHEDRAL : 17.301 276 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 6DGA 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_1000234563. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-JUN-16 REMARK 200 TEMPERATURE (KELVIN) : 93 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL14-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.18076 REMARK 200 MONOCHROMATOR : SI (111) DOUBLE CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 325 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26581 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.190 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 (%) : 96.7 REMARK 200 DATA REDUNDANCY : 6.800 REMARK 200 R MERGE (I) : 0.06700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.19 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.21 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.70 REMARK 200 R MERGE FOR SHELL (I) : 0.48900 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: NULL 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 (%): 38.82 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.01 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 75 MM NAH2PO4, 20% (VOL/VOL) PEG 3350, REMARK 280 1 MM BDSF, AND 0.62% (VOL/VOL) DMSO, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 27.48800 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.81950 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.48800 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.81950 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 HH11 ARG A 22 O HOH A 101 1.53 REMARK 500 REMARK 500 REMARK: NULL DBREF 6DGA A 1 95 UNP C9XTL5 C9XTL5_CROTZ 21 115 SEQRES 1 A 95 MET LYS ASP ASP LEU ASP ASN ASN LEU LEU TYR ARG TYR SEQRES 2 A 95 CYS GLY ALA THR SER PRO PHE TRP ARG LEU PRO LEU ASP SEQRES 3 A 95 SER ASN ALA LEU GLN LEU ALA ALA SER GLU GLU ALA VAL SEQRES 4 A 95 THR SER HIS VAL VAL PRO LEU THR PRO GLU GLN ALA ALA SEQRES 5 A 95 GLN ILE ARG THR MET SER VAL ILE THR SER SER VAL THR SEQRES 6 A 95 LEU SER LEU SER LEU PHE GLY GLU LEU VAL PRO VAL HIS SEQRES 7 A 95 LEU VAL GLY ARG LYS VAL SER ARG LYS GLU TRP ALA GLY SEQRES 8 A 95 THR ALA SER ALA FORMUL 2 HOH *118(H2 O) HELIX 1 AA1 ASN A 8 GLY A 15 1 8 HELIX 2 AA2 THR A 47 ARG A 55 1 9 SHEET 1 AA1 6 HIS A 42 PRO A 45 0 SHEET 2 AA1 6 ALA A 29 ALA A 33 -1 N LEU A 30 O VAL A 44 SHEET 3 AA1 6 PHE A 20 PRO A 24 -1 N PHE A 20 O ALA A 33 SHEET 4 AA1 6 GLU A 88 SER A 94 -1 O TRP A 89 N LEU A 23 SHEET 5 AA1 6 GLU A 73 SER A 85 -1 N VAL A 80 O THR A 92 SHEET 6 AA1 6 SER A 62 LEU A 70 -1 N VAL A 64 O LEU A 79 CRYST1 54.976 53.639 28.197 90.00 90.00 90.00 P 21 21 2 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 0.018190 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018643 0.000000 0.00000 SCALE3 0.000000 0.000000 0.035465 0.00000