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- PDB-3qp5: Crystal structure of CviR bound to antagonist chlorolactone (CL) -

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Basic information

Entry
Database: PDB / ID: 3qp5
TitleCrystal structure of CviR bound to antagonist chlorolactone (CL)
ComponentsCviR transcriptional regulator
KeywordsTRANSCRIPTION / quorum sensing / agonist / antagonist / LuxR / acylated homoserine lactone / transcription factor / DNA binding protein / ligand binding domain / signal receptor / Quorum sensing transcription factor / chlorolactone (CL)
Function / homology
Function and homology information


regulation of DNA-templated transcription / DNA binding
Similarity search - Function
Transcription factor LuxR-like, autoinducer-binding domain / Transcription factor LuxR-like, autoinducer-binding domain / Transcription factor LuxR-like, autoinducer-binding domain superfamily / Autoinducer binding domain / LuxR-type HTH domain signature. / LuxR-type HTH domain profile. / Transcription regulator LuxR, C-terminal / Bacterial regulatory proteins, luxR family / helix_turn_helix, Lux Regulon / Signal transduction response regulator, C-terminal effector ...Transcription factor LuxR-like, autoinducer-binding domain / Transcription factor LuxR-like, autoinducer-binding domain / Transcription factor LuxR-like, autoinducer-binding domain superfamily / Autoinducer binding domain / LuxR-type HTH domain signature. / LuxR-type HTH domain profile. / Transcription regulator LuxR, C-terminal / Bacterial regulatory proteins, luxR family / helix_turn_helix, Lux Regulon / Signal transduction response regulator, C-terminal effector / Beta-Lactamase / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-HLC / CviR transcriptional regulator
Similarity search - Component
Biological speciesChromobacterium violaceum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.249 Å
AuthorsChen, G. / Swem, L. / Swem, D. / Stauff, D. / O'Loughlin, C. / Jeffrey, P. / Bassler, B. / Hughson, F.
CitationJournal: Mol.Cell / Year: 2011
Title: A strategy for antagonizing quorum sensing.
Authors: Chen, G. / Swem, L.R. / Swem, D.L. / Stauff, D.L. / O'Loughlin, C.T. / Jeffrey, P.D. / Bassler, B.L. / Hughson, F.M.
History
DepositionFeb 11, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CviR transcriptional regulator
B: CviR transcriptional regulator
C: CviR transcriptional regulator
D: CviR transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,2038
Polymers119,0124
Non-polymers1,1914
Water0
1
A: CviR transcriptional regulator
B: CviR transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,1024
Polymers59,5062
Non-polymers5952
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4290 Å2
ΔGint-19 kcal/mol
Surface area23270 Å2
MethodPISA
2
C: CviR transcriptional regulator
D: CviR transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,1024
Polymers59,5062
Non-polymers5952
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4240 Å2
ΔGint-28 kcal/mol
Surface area23040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)169.318, 169.318, 99.844
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein
CviR transcriptional regulator / Transcriptional activator / LuxR/UhpA family of regulators


Mass: 29753.018 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chromobacterium violaceum (bacteria) / Strain: 31532 / Gene: cviR / Plasmid: pET23b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon plus / References: UniProt: D3W065
#2: Chemical
ChemComp-HLC / 4-(4-chlorophenoxy)-N-[(3S)-2-oxotetrahydrofuran-3-yl]butanamide


Mass: 297.734 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H16ClNO4

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.85 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 50 mM sodium citrate, 15-20% w/v PEG3350, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 18, 2009
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 3.249→84.659 Å / Num. obs: 16715 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.5 % / Rmerge(I) obs: 0.062 / Rsym value: 0.062 / Net I/σ(I): 16.851
Reflection shellResolution: 3.25→3.37 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.488 / Mean I/σ(I) obs: 2.855 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.5_2)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3QP1

3qp1


Resolution: 3.249→48.878 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.51 / σ(F): 0.03 / Phase error: 34.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3036 808 5.06 %
Rwork0.2631 --
obs0.2652 15970 94.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 95.363 Å2 / ksol: 0.306 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--16.5656 Å20 Å20 Å2
2---16.5656 Å2-0 Å2
3---33.1312 Å2
Refinement stepCycle: LAST / Resolution: 3.249→48.878 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7658 0 80 0 7738
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0127900
X-RAY DIFFRACTIONf_angle_d1.89610697
X-RAY DIFFRACTIONf_dihedral_angle_d17.8982918
X-RAY DIFFRACTIONf_chiral_restr0.1711170
X-RAY DIFFRACTIONf_plane_restr0.0131397
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2489-3.45240.35361200.31882163X-RAY DIFFRACTION81
3.4524-3.71890.39471380.29552488X-RAY DIFFRACTION95
3.7189-4.0930.29711350.26772592X-RAY DIFFRACTION97
4.093-4.68480.28681330.24132632X-RAY DIFFRACTION99
4.6848-5.90080.3131380.25082663X-RAY DIFFRACTION100
5.9008-48.88340.25951440.25022624X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.0451.86811.12264.36060.17161.3124-0.2925-0.0139-0.5788-0.07620.3657-0.5245-0.1380.1463-0.10450.38960.02270.14760.1007-0.14830.374632.69724.1467-1.364
20.6751-1.20220.39362.36990.22613.92960.24670.0397-0.61330.0339-0.0559-1.4719-0.15440.39950.04550.5019-0.1258-0.47570.48290.23581.508646.8137-13.053327.4177
32.26551.29771.14552.8999-1.10892.0723-0.0093-0.2156-0.4565-0.13520.01830.89080.3423-0.31140.00350.45360.00660.21170.4406-0.18021.20715.313521.004827.087
42.32131.6791-0.6814.1704-3.03423.7204-0.59190.53550.2147-0.0815-0.3015-0.0448-0.09170.03220.62540.2809-0.0223-0.08590.34860.07220.416738.07847.042717.1806
52.7773-2.44510.87176.8232.51753.0338-0.34370.4499-0.70311.67650.29921.66230.11130.6008-0.15271.3279-0.3948-0.13370.72990.37741.052329.5636-4.885144.9255
67.10241.69413.71041.00192.71078.4622-0.07970.2738-1.85280.45410.5451-0.13741.27610.70080.84210.32820.10980.37570.10890.16110.811145.861827.09641.2546
77.181-3.44356.5223.5504-4.59728.4903-0.69490.05132.1381-0.853-0.958-0.052-0.241-0.3837-0.21270.59810.1612-0.49030.0246-0.11310.507521.11467.687915.889
86.0823-0.9624-1.44720.97431.03752.5273-0.91330.1165-1.67540.89270.522-0.90410.9920.28730.42050.5725-0.13970.04440.4266-0.43140.90043.890415.1583.129
94.45733.75384.53086.14627.92142-1.8744-0.21380.1855-0.47760.00350.2368-0.141-0.86661.66843.9829-0.22960.02780.6512-0.45041.207630.854212.4623-4.6418
103.34952.0226-0.35761.2586-0.32530.35520.29390.1517-0.36340.4936-0.7064-0.27490.78670.2046-0.02131.7318-0.6175-0.55881.6530.25412.450747.115-13.163836.3352
119.513-4.68053.38773.63780.45467.19661.78870.9493-0.6792-0.2105-0.5211-0.9652-0.7167-2.7999-0.9220.67060.14040.43771.12220.28131.56228.153916.626324.4247
122.1297-0.67520.14670.62970.36170.53270.35430.14810.08190.5916-0.1804-0.276-0.3202-1.7772-0.12891.0457-0.8341-0.07042.72670.47080.636538.482755.576313.58
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A resid 8:191
2X-RAY DIFFRACTION2chain B resid 14:189
3X-RAY DIFFRACTION3chain C resid 11:191
4X-RAY DIFFRACTION4chain D resid 10:188
5X-RAY DIFFRACTION5chain A resid 197:259
6X-RAY DIFFRACTION6chain B resid 197:258
7X-RAY DIFFRACTION7chain C resid 197:259
8X-RAY DIFFRACTION8chain D resid 197:255
9X-RAY DIFFRACTION9chain E
10X-RAY DIFFRACTION10chain F
11X-RAY DIFFRACTION11chain G
12X-RAY DIFFRACTION12chain H

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