HEADER TRANSCRIPTION 11-FEB-11 3QP8 TITLE CRYSTAL STRUCTURE OF CVIR (CHROMOBACTERIUM VIOLACEUM 12472) LIGAND- TITLE 2 BINDING DOMAIN BOUND TO C10-HSL COMPND MOL_ID: 1; COMPND 2 MOLECULE: CVIR TRANSCRIPTIONAL REGULATOR; COMPND 3 CHAIN: A, B, C, D; COMPND 4 FRAGMENT: LIGAND BINDING DOMAIN (UNP RESIDUES 8-187); COMPND 5 SYNONYM: TRANSCRIPTIONAL ACTIVATOR, LUXR/UHPA FAMILY OF REGULATORS; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CHROMOBACTERIUM VIOLACEUM; SOURCE 3 ORGANISM_TAXID: 536; SOURCE 4 STRAIN: 12472; SOURCE 5 GENE: CVIR; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)PLYSS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28B KEYWDS QUORUM SENSING, AGONIST, ANTAGONIST, LUXR, ACYLATED HOMOSERINE KEYWDS 2 LACTONE, TRANSCRIPTION FACTOR, DNA BINDING PROTEIN, LIGAND BINDING KEYWDS 3 DOMAIN, SIGNAL RECEPTOR, QUORUM SENSING TRANSCRIPTION RECEPTOR, N- KEYWDS 4 DECANOYL-L-HOMOSERINE LACTONE, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR G.CHEN,L.SWEM,D.SWEM,D.STAUFF,C.O'LOUGHLIN,P.JEFFREY,B.BASSLER, AUTHOR 2 F.HUGHSON REVDAT 3 13-SEP-23 3QP8 1 REMARK SEQADV REVDAT 2 04-MAY-11 3QP8 1 JRNL REVDAT 1 30-MAR-11 3QP8 0 JRNL AUTH G.CHEN,L.R.SWEM,D.L.SWEM,D.L.STAUFF,C.T.O'LOUGHLIN, JRNL AUTH 2 P.D.JEFFREY,B.L.BASSLER,F.M.HUGHSON JRNL TITL A STRATEGY FOR ANTAGONIZING QUORUM SENSING. JRNL REF MOL.CELL V. 42 199 2011 JRNL REFN ISSN 1097-2765 JRNL PMID 21504831 JRNL DOI 10.1016/J.MOLCEL.2011.04.003 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 70.71 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 100970 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.199 REMARK 3 R VALUE (WORKING SET) : 0.198 REMARK 3 FREE R VALUE : 0.230 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 5043 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.64 REMARK 3 REFLECTION IN BIN (WORKING SET) : 6827 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.73 REMARK 3 BIN R VALUE (WORKING SET) : 0.2540 REMARK 3 BIN FREE R VALUE SET COUNT : 397 REMARK 3 BIN FREE R VALUE : 0.2900 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5648 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 72 REMARK 3 SOLVENT ATOMS : 470 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.04 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.56000 REMARK 3 B22 (A**2) : -0.48000 REMARK 3 B33 (A**2) : -0.35000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -1.67000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.095 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.095 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.068 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.879 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.964 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.951 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5834 ; 0.010 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7883 ; 1.277 ; 1.948 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 724 ; 5.614 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 281 ;39.363 ;24.377 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 980 ;13.282 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 44 ;12.508 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 850 ; 0.080 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4464 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2711 ; 0.206 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 4005 ; 0.304 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 406 ; 0.130 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 83 ; 0.209 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 29 ; 0.165 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 5 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 9 A 187 REMARK 3 ORIGIN FOR THE GROUP (A): 9.8180 19.6810 41.0640 REMARK 3 T TENSOR REMARK 3 T11: 0.0133 T22: -0.0353 REMARK 3 T33: -0.0021 T12: -0.0058 REMARK 3 T13: 0.0655 T23: 0.0115 REMARK 3 L TENSOR REMARK 3 L11: 1.9792 L22: 0.8905 REMARK 3 L33: 1.3292 L12: -0.0552 REMARK 3 L13: -0.0963 L23: -0.2230 REMARK 3 S TENSOR REMARK 3 S11: -0.1176 S12: -0.0774 S13: 0.1394 REMARK 3 S21: 0.0457 S22: 0.0085 S23: -0.1684 REMARK 3 S31: -0.1428 S32: 0.2732 S33: 0.1090 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 4 B 187 REMARK 3 ORIGIN FOR THE GROUP (A): -15.8500 3.7270 25.0720 REMARK 3 T TENSOR REMARK 3 T11: -0.0020 T22: -0.0892 REMARK 3 T33: -0.0435 T12: -0.0193 REMARK 3 T13: 0.1060 T23: 0.0128 REMARK 3 L TENSOR REMARK 3 L11: 1.3111 L22: 1.5315 REMARK 3 L33: 1.3818 L12: 0.8260 REMARK 3 L13: 0.8420 L23: 0.6230 REMARK 3 S TENSOR REMARK 3 S11: -0.0789 S12: 0.0263 S13: -0.0054 REMARK 3 S21: -0.1319 S22: 0.0948 S23: 0.0307 REMARK 3 S31: 0.0956 S32: -0.0917 S33: -0.0159 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : C 7 C 187 REMARK 3 ORIGIN FOR THE GROUP (A): -9.5630 39.6350 4.5110 REMARK 3 T TENSOR REMARK 3 T11: 0.1141 T22: -0.0326 REMARK 3 T33: -0.0147 T12: -0.0404 REMARK 3 T13: 0.1216 T23: 0.0504 REMARK 3 L TENSOR REMARK 3 L11: 1.4337 L22: 1.4808 REMARK 3 L33: 1.3335 L12: -1.0112 REMARK 3 L13: 0.2950 L23: -0.5836 REMARK 3 S TENSOR REMARK 3 S11: 0.0547 S12: -0.0187 S13: -0.0243 REMARK 3 S21: 0.1341 S22: 0.0323 S23: 0.1959 REMARK 3 S31: -0.3077 S32: -0.1476 S33: -0.0870 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : D 4 D 187 REMARK 3 ORIGIN FOR THE GROUP (A): 22.4740 31.1500 14.5090 REMARK 3 T TENSOR REMARK 3 T11: 0.0650 T22: 0.0213 REMARK 3 T33: -0.0213 T12: -0.1307 REMARK 3 T13: 0.1400 T23: -0.0530 REMARK 3 L TENSOR REMARK 3 L11: 1.9658 L22: 1.3300 REMARK 3 L33: 0.6668 L12: 1.2142 REMARK 3 L13: 0.7939 L23: 0.5606 REMARK 3 S TENSOR REMARK 3 S11: -0.2797 S12: 0.3087 S13: -0.2402 REMARK 3 S21: -0.2913 S22: 0.3748 S23: -0.2789 REMARK 3 S31: -0.1279 S32: 0.2204 S33: -0.0951 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 4 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 1 REMARK 3 RESIDUE RANGE : B 2 B 2 REMARK 3 RESIDUE RANGE : C 3 C 3 REMARK 3 RESIDUE RANGE : D 188 D 188 REMARK 3 ORIGIN FOR THE GROUP (A): 3.3410 23.9520 18.7460 REMARK 3 T TENSOR REMARK 3 T11: 0.1056 T22: -0.0162 REMARK 3 T33: 0.1073 T12: -0.0004 REMARK 3 T13: 0.1224 T23: -0.0223 REMARK 3 L TENSOR REMARK 3 L11: 0.1844 L22: 0.1054 REMARK 3 L33: 0.6331 L12: 0.1215 REMARK 3 L13: -0.2270 L23: -0.0550 REMARK 3 S TENSOR REMARK 3 S11: -0.0124 S12: 0.0190 S13: -0.0375 REMARK 3 S21: -0.0374 S22: 0.0746 S23: -0.0633 REMARK 3 S31: -0.0821 S32: 0.0459 S33: -0.0621 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3QP8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-FEB-11. REMARK 100 THE DEPOSITION ID IS D_1000063929. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-OCT-08 REMARK 200 TEMPERATURE (KELVIN) : 298 REMARK 200 PH : 9.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X25 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0809 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 101162 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 70.710 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.04300 REMARK 200 FOR THE DATA SET : 16.6780 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.66 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.5 REMARK 200 DATA REDUNDANCY IN SHELL : 3.50 REMARK 200 R MERGE FOR SHELL (I) : 0.39700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.250 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: PDB ENTRY 3QP6 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.36 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.38 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM CHES, 1 M SODIUM CITRATE, PH REMARK 280 9.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 296K 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 35.80650 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2560 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16620 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -16.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2870 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16480 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -14.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D 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 GLY A 4 REMARK 465 SER A 5 REMARK 465 HIS A 6 REMARK 465 MET A 7 REMARK 465 ASN A 8 REMARK 465 GLY C 4 REMARK 465 SER C 5 REMARK 465 HIS C 6 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 O ALA A 94 NH2 ARG A 101 2.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 ASN D 64 CG ASN D 64 ND2 0.208 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 PRO A 161 C - N - CA ANGL. DEV. = 12.6 DEGREES 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 SER A 49 39.38 -68.23 REMARK 500 PRO A 52 -97.17 -97.18 REMARK 500 SER A 53 36.14 -87.54 REMARK 500 SER A 79 25.96 -152.73 REMARK 500 LYS A 159 -74.19 -55.13 REMARK 500 PRO A 161 -71.75 -32.10 REMARK 500 SER B 79 15.72 -148.01 REMARK 500 ASN C 8 34.96 -92.83 REMARK 500 SER C 79 21.08 -152.45 REMARK 500 PRO C 161 -70.68 -33.16 REMARK 500 SER D 79 20.80 -152.40 REMARK 500 ARG D 163 -64.43 61.06 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLU C 160 PRO C 161 -136.56 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 HL0 A 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HL0 B 2 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HL0 C 3 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HL0 D 188 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3QP1 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF CVIR LIGAND-BINDING DOMAIN BOUND TO C6-HSL REMARK 900 RELATED ID: 3QP2 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF CVIR LIGAND-BINDING DOMAIN BOUND TO C8-HSL REMARK 900 RELATED ID: 3QP4 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF CVIR LIGAND-BINDING DOMAIN BOUND TO C10-HSL REMARK 900 RELATED ID: 3QP5 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF CVIR BOUND TO ANTAGONIST CHLOROLACTONE (CL) REMARK 900 RELATED ID: 3QP6 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF CVIR (CHROMOBACTERIUM VIOLACEUM 12472) BOUND REMARK 900 TO C6-HSL REMARK 900 RELATED ID: 3QP7 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF SEMET CVIR (CHROMOBACTERIUM VIOLACEUM 12472) REMARK 900 BOUND TO C6-HSL DBREF 3QP8 A 8 187 UNP Q7NQP7 Q7NQP7_CHRVO 8 187 DBREF 3QP8 B 8 187 UNP Q7NQP7 Q7NQP7_CHRVO 8 187 DBREF 3QP8 C 8 187 UNP Q7NQP7 Q7NQP7_CHRVO 8 187 DBREF 3QP8 D 8 187 UNP Q7NQP7 Q7NQP7_CHRVO 8 187 SEQADV 3QP8 GLY A 4 UNP Q7NQP7 EXPRESSION TAG SEQADV 3QP8 SER A 5 UNP Q7NQP7 EXPRESSION TAG SEQADV 3QP8 HIS A 6 UNP Q7NQP7 EXPRESSION TAG SEQADV 3QP8 MET A 7 UNP Q7NQP7 EXPRESSION TAG SEQADV 3QP8 GLY B 4 UNP Q7NQP7 EXPRESSION TAG SEQADV 3QP8 SER B 5 UNP Q7NQP7 EXPRESSION TAG SEQADV 3QP8 HIS B 6 UNP Q7NQP7 EXPRESSION TAG SEQADV 3QP8 MET B 7 UNP Q7NQP7 EXPRESSION TAG SEQADV 3QP8 GLY C 4 UNP Q7NQP7 EXPRESSION TAG SEQADV 3QP8 SER C 5 UNP Q7NQP7 EXPRESSION TAG SEQADV 3QP8 HIS C 6 UNP Q7NQP7 EXPRESSION TAG SEQADV 3QP8 MET C 7 UNP Q7NQP7 EXPRESSION TAG SEQADV 3QP8 GLY D 4 UNP Q7NQP7 EXPRESSION TAG SEQADV 3QP8 SER D 5 UNP Q7NQP7 EXPRESSION TAG SEQADV 3QP8 HIS D 6 UNP Q7NQP7 EXPRESSION TAG SEQADV 3QP8 MET D 7 UNP Q7NQP7 EXPRESSION TAG SEQRES 1 A 184 GLY SER HIS MET ASN ALA ARG PRO LEU PRO ALA GLY LEU SEQRES 2 A 184 THR ALA SER GLN GLN TRP THR LEU LEU GLU TRP ILE HIS SEQRES 3 A 184 MET ALA GLY HIS ILE GLU THR GLU GLY GLU LEU LYS ALA SEQRES 4 A 184 PHE LEU ASP ASN ILE LEU SER GLN ALA PRO SER ASP ARG SEQRES 5 A 184 ILE ILE LEU VAL LEU GLY ARG LEU ASN ASN GLN ASN GLN SEQRES 6 A 184 ILE GLN ARG MET GLU LYS VAL LEU ASN VAL SER TYR PRO SEQRES 7 A 184 SER ASP TRP LEU ASN GLN TYR SER GLN GLU ASN PHE ALA SEQRES 8 A 184 GLN HIS ASP PRO ILE MET ARG ILE HIS LEU GLY GLN GLY SEQRES 9 A 184 PRO VAL ILE TRP GLU GLU ARG PHE SER ARG ALA LYS GLY SEQRES 10 A 184 SER GLU GLU LYS ARG PHE ILE ALA GLU ALA SER SER ASN SEQRES 11 A 184 GLY MET GLY SER GLY ILE THR PHE SER ALA ALA SER ASP SEQRES 12 A 184 ARG ASN ASN VAL GLY SER ILE LEU SER ILE GLY GLY LYS SEQRES 13 A 184 GLU PRO GLY ARG ASN ALA ALA LEU VAL ALA MET LEU ASN SEQRES 14 A 184 CYS LEU THR PRO HIS LEU HIS GLN ALA ALA VAL ARG ILE SEQRES 15 A 184 ALA ASN SEQRES 1 B 184 GLY SER HIS MET ASN ALA ARG PRO LEU PRO ALA GLY LEU SEQRES 2 B 184 THR ALA SER GLN GLN TRP THR LEU LEU GLU TRP ILE HIS SEQRES 3 B 184 MET ALA GLY HIS ILE GLU THR GLU GLY GLU LEU LYS ALA SEQRES 4 B 184 PHE LEU ASP ASN ILE LEU SER GLN ALA PRO SER ASP ARG SEQRES 5 B 184 ILE ILE LEU VAL LEU GLY ARG LEU ASN ASN GLN ASN GLN SEQRES 6 B 184 ILE GLN ARG MET GLU LYS VAL LEU ASN VAL SER TYR PRO SEQRES 7 B 184 SER ASP TRP LEU ASN GLN TYR SER GLN GLU ASN PHE ALA SEQRES 8 B 184 GLN HIS ASP PRO ILE MET ARG ILE HIS LEU GLY GLN GLY SEQRES 9 B 184 PRO VAL ILE TRP GLU GLU ARG PHE SER ARG ALA LYS GLY SEQRES 10 B 184 SER GLU GLU LYS ARG PHE ILE ALA GLU ALA SER SER ASN SEQRES 11 B 184 GLY MET GLY SER GLY ILE THR PHE SER ALA ALA SER ASP SEQRES 12 B 184 ARG ASN ASN VAL GLY SER ILE LEU SER ILE GLY GLY LYS SEQRES 13 B 184 GLU PRO GLY ARG ASN ALA ALA LEU VAL ALA MET LEU ASN SEQRES 14 B 184 CYS LEU THR PRO HIS LEU HIS GLN ALA ALA VAL ARG ILE SEQRES 15 B 184 ALA ASN SEQRES 1 C 184 GLY SER HIS MET ASN ALA ARG PRO LEU PRO ALA GLY LEU SEQRES 2 C 184 THR ALA SER GLN GLN TRP THR LEU LEU GLU TRP ILE HIS SEQRES 3 C 184 MET ALA GLY HIS ILE GLU THR GLU GLY GLU LEU LYS ALA SEQRES 4 C 184 PHE LEU ASP ASN ILE LEU SER GLN ALA PRO SER ASP ARG SEQRES 5 C 184 ILE ILE LEU VAL LEU GLY ARG LEU ASN ASN GLN ASN GLN SEQRES 6 C 184 ILE GLN ARG MET GLU LYS VAL LEU ASN VAL SER TYR PRO SEQRES 7 C 184 SER ASP TRP LEU ASN GLN TYR SER GLN GLU ASN PHE ALA SEQRES 8 C 184 GLN HIS ASP PRO ILE MET ARG ILE HIS LEU GLY GLN GLY SEQRES 9 C 184 PRO VAL ILE TRP GLU GLU ARG PHE SER ARG ALA LYS GLY SEQRES 10 C 184 SER GLU GLU LYS ARG PHE ILE ALA GLU ALA SER SER ASN SEQRES 11 C 184 GLY MET GLY SER GLY ILE THR PHE SER ALA ALA SER ASP SEQRES 12 C 184 ARG ASN ASN VAL GLY SER ILE LEU SER ILE GLY GLY LYS SEQRES 13 C 184 GLU PRO GLY ARG ASN ALA ALA LEU VAL ALA MET LEU ASN SEQRES 14 C 184 CYS LEU THR PRO HIS LEU HIS GLN ALA ALA VAL ARG ILE SEQRES 15 C 184 ALA ASN SEQRES 1 D 184 GLY SER HIS MET ASN ALA ARG PRO LEU PRO ALA GLY LEU SEQRES 2 D 184 THR ALA SER GLN GLN TRP THR LEU LEU GLU TRP ILE HIS SEQRES 3 D 184 MET ALA GLY HIS ILE GLU THR GLU GLY GLU LEU LYS ALA SEQRES 4 D 184 PHE LEU ASP ASN ILE LEU SER GLN ALA PRO SER ASP ARG SEQRES 5 D 184 ILE ILE LEU VAL LEU GLY ARG LEU ASN ASN GLN ASN GLN SEQRES 6 D 184 ILE GLN ARG MET GLU LYS VAL LEU ASN VAL SER TYR PRO SEQRES 7 D 184 SER ASP TRP LEU ASN GLN TYR SER GLN GLU ASN PHE ALA SEQRES 8 D 184 GLN HIS ASP PRO ILE MET ARG ILE HIS LEU GLY GLN GLY SEQRES 9 D 184 PRO VAL ILE TRP GLU GLU ARG PHE SER ARG ALA LYS GLY SEQRES 10 D 184 SER GLU GLU LYS ARG PHE ILE ALA GLU ALA SER SER ASN SEQRES 11 D 184 GLY MET GLY SER GLY ILE THR PHE SER ALA ALA SER ASP SEQRES 12 D 184 ARG ASN ASN VAL GLY SER ILE LEU SER ILE GLY GLY LYS SEQRES 13 D 184 GLU PRO GLY ARG ASN ALA ALA LEU VAL ALA MET LEU ASN SEQRES 14 D 184 CYS LEU THR PRO HIS LEU HIS GLN ALA ALA VAL ARG ILE SEQRES 15 D 184 ALA ASN HET HL0 A 1 18 HET HL0 B 2 18 HET HL0 C 3 18 HET HL0 D 188 18 HETNAM HL0 N-[(3S)-2-OXOTETRAHYDROFURAN-3-YL]DECANAMIDE HETSYN HL0 N-DECANOYL-L-HOMOSERINE LACTONE FORMUL 5 HL0 4(C14 H25 N O3) FORMUL 9 HOH *470(H2 O) HELIX 1 1 THR A 17 GLY A 32 1 16 HELIX 2 2 THR A 36 SER A 49 1 14 HELIX 3 3 PRO A 81 GLU A 91 1 11 HELIX 4 4 ASN A 92 HIS A 96 5 5 HELIX 5 5 ASP A 97 ILE A 102 5 6 HELIX 6 6 TRP A 111 ARG A 117 1 7 HELIX 7 7 GLY A 120 SER A 132 1 13 HELIX 8 8 ASN A 164 ASN A 187 1 24 HELIX 9 9 THR B 17 GLY B 32 1 16 HELIX 10 10 THR B 36 SER B 49 1 14 HELIX 11 11 PRO B 81 GLU B 91 1 11 HELIX 12 12 ASN B 92 HIS B 96 5 5 HELIX 13 13 ASP B 97 ILE B 102 5 6 HELIX 14 14 TRP B 111 SER B 116 1 6 HELIX 15 15 GLY B 120 SER B 132 1 13 HELIX 16 16 GLU B 160 ARG B 163 5 4 HELIX 17 17 ASN B 164 ASN B 187 1 24 HELIX 18 18 THR C 17 GLY C 32 1 16 HELIX 19 19 THR C 36 LEU C 48 1 13 HELIX 20 20 PRO C 81 GLU C 91 1 11 HELIX 21 21 ASN C 92 HIS C 96 5 5 HELIX 22 22 ASP C 97 ILE C 102 5 6 HELIX 23 23 TRP C 111 ALA C 118 1 8 HELIX 24 24 GLY C 120 ASN C 133 1 14 HELIX 25 25 ASN C 164 ASN C 187 1 24 HELIX 26 26 THR D 17 GLY D 32 1 16 HELIX 27 27 THR D 36 SER D 49 1 14 HELIX 28 28 PRO D 81 GLU D 91 1 11 HELIX 29 29 ASN D 92 HIS D 96 5 5 HELIX 30 30 ASP D 97 ILE D 102 5 6 HELIX 31 31 TRP D 111 SER D 116 1 6 HELIX 32 32 GLY D 120 ASN D 133 1 14 HELIX 33 33 ASN D 164 ASN D 187 1 24 SHEET 1 A 5 ILE A 69 ASN A 77 0 SHEET 2 A 5 ARG A 55 LEU A 63 -1 N LEU A 58 O LEU A 76 SHEET 3 A 5 VAL A 150 GLY A 157 -1 O GLY A 157 N ARG A 55 SHEET 4 A 5 GLY A 138 SER A 145 -1 N PHE A 141 O LEU A 154 SHEET 5 A 5 VAL A 109 ILE A 110 -1 N VAL A 109 O THR A 140 SHEET 1 B 5 ILE B 69 ASN B 77 0 SHEET 2 B 5 ILE B 56 LEU B 63 -1 N ARG B 62 O GLN B 70 SHEET 3 B 5 VAL B 150 GLY B 157 -1 O GLY B 151 N GLY B 61 SHEET 4 B 5 GLY B 138 ALA B 144 -1 N PHE B 141 O LEU B 154 SHEET 5 B 5 VAL B 109 ILE B 110 -1 N VAL B 109 O THR B 140 SHEET 1 C 5 ILE C 69 ASN C 77 0 SHEET 2 C 5 ARG C 55 LEU C 63 -1 N ARG C 62 O ARG C 71 SHEET 3 C 5 VAL C 150 GLY C 157 -1 O GLY C 151 N GLY C 61 SHEET 4 C 5 GLY C 138 ALA C 144 -1 N PHE C 141 O LEU C 154 SHEET 5 C 5 VAL C 109 ILE C 110 -1 N VAL C 109 O THR C 140 SHEET 1 D 5 ILE D 69 ASN D 77 0 SHEET 2 D 5 ARG D 55 LEU D 63 -1 N LEU D 58 O LEU D 76 SHEET 3 D 5 VAL D 150 GLY D 157 -1 O GLY D 157 N ARG D 55 SHEET 4 D 5 GLY D 138 SER D 145 -1 N SER D 145 O VAL D 150 SHEET 5 D 5 VAL D 109 ILE D 110 -1 N VAL D 109 O THR D 140 CISPEP 1 LEU C 104 GLY C 105 0 -24.55 SITE 1 AC1 10 TYR A 80 TRP A 84 TYR A 88 ASP A 97 SITE 2 AC1 10 ILE A 99 TRP A 111 MET A 135 ILE A 153 SITE 3 AC1 10 SER A 155 PRO D 52 SITE 1 AC2 11 TYR B 80 TRP B 84 LEU B 85 TYR B 88 SITE 2 AC2 11 ASP B 97 ILE B 99 PHE B 126 ALA B 130 SITE 3 AC2 11 MET B 135 ILE B 153 SER B 155 SITE 1 AC3 11 TYR C 80 TRP C 84 ASP C 97 ILE C 99 SITE 2 AC3 11 MET C 100 TRP C 111 PHE C 115 PHE C 126 SITE 3 AC3 11 MET C 135 ILE C 153 SER C 155 SITE 1 AC4 9 TYR D 80 TRP D 84 ASP D 97 MET D 100 SITE 2 AC4 9 TRP D 111 PHE D 115 MET D 135 ILE D 153 SITE 3 AC4 9 SER D 155 CRYST1 76.461 71.613 77.737 90.00 114.58 90.00 P 1 21 1 8 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 0.013079 0.000000 0.005983 0.00000 SCALE2 0.000000 0.013964 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014146 0.00000