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- PDB-3qp2: Crystal structure of CviR ligand-binding domain bound to C8-HSL -

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Basic information

Entry
Database: PDB / ID: 3qp2
TitleCrystal structure of CviR ligand-binding domain bound to C8-HSL
ComponentsCviR transcriptional regulator
KeywordsTRANSCRIPTION / quorum sensing / agonist / antagonist / LuxR / acylated homoserine lactone / transcription factor / DNA binding protein / ligand binding domain / signal receptor / transcription activator / N-hexanoyl-L-homoserine lactone
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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
N-(2-OXOTETRAHYDROFURAN-3-YL)OCTANAMIDE / CviR transcriptional regulator
Similarity search - Component
Biological speciesChromobacterium violaceum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.638 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: CviR transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6082
Polymers20,3811
Non-polymers2271
Water1,71195
1
A: CviR transcriptional regulator
hetero molecules

A: CviR transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2174
Polymers40,7622
Non-polymers4552
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area3550 Å2
ΔGint-8 kcal/mol
Surface area16490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.580, 55.907, 124.988
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-191-

HOH

21A-198-

HOH

31A-199-

HOH

41A-217-

HOH

51A-271-

HOH

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Components

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


Mass: 20381.113 Da / Num. of mol.: 1 / Fragment: ligand binding domain (UNP residues 10-187)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chromobacterium violaceum (bacteria) / Strain: 31532 / Gene: cviR / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / References: UniProt: D3W065
#2: Chemical ChemComp-HTF / N-(2-OXOTETRAHYDROFURAN-3-YL)OCTANAMIDE / N-OCTANOYL-L-HOMOSERINE LACTONE


Mass: 227.300 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H21NO3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 95 / Source method: isolated from a natural source / Formula: H2O

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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: 2.39 Å3/Da / Density % sol: 48.43 %
Crystal growTemperature: 296 K / Method: vapor diffusion / pH: 9
Details: 100 mM Tris-Cl, 200 mM magnesium chloride, 25-35% w/v PEG3350, pH 9.0, VAPOR DIFFUSION, temperature 296K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.0809
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 27, 2009
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0809 Å / Relative weight: 1
ReflectionResolution: 1.638→62.494 Å / Num. all: 24394 / Num. obs: 24191 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.8 % / Rmerge(I) obs: 0.06 / Rsym value: 0.084 / Net I/σ(I): 15.9
Reflection shellResolution: 1.64→1.7 Å / Rmerge(I) obs: 0.498 / Mean I/σ(I) obs: 2.194 / % possible all: 99.5

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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: 1.638→33.407 Å / SU ML: 0.19 / Phase error: 21.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2227 1197 5.11 %RANDOM
Rwork0.2006 ---
obs0.2017 23404 96.05 %-
all-24191 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 65.016 Å2 / ksol: 0.412 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.3537 Å20 Å2-0 Å2
2--3.4741 Å20 Å2
3----3.1204 Å2
Refinement stepCycle: LAST / Resolution: 1.638→33.407 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1403 0 16 95 1514
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061456
X-RAY DIFFRACTIONf_angle_d1.0761970
X-RAY DIFFRACTIONf_dihedral_angle_d16.962550
X-RAY DIFFRACTIONf_chiral_restr0.069213
X-RAY DIFFRACTIONf_plane_restr0.004261
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6384-1.7040.33281130.2482197X-RAY DIFFRACTION88
1.704-1.78150.19461280.2132340X-RAY DIFFRACTION92
1.7815-1.87550.2171240.192405X-RAY DIFFRACTION94
1.8755-1.9930.2261460.19112468X-RAY DIFFRACTION98
1.993-2.14680.20631500.18252498X-RAY DIFFRACTION99
2.1468-2.36280.20591330.18392529X-RAY DIFFRACTION99
2.3628-2.70460.25011300.1942561X-RAY DIFFRACTION99
2.7046-3.40690.23981340.19882607X-RAY DIFFRACTION100
3.4069-33.41370.20141390.20252602X-RAY DIFFRACTION96
Refinement TLS params.Method: refined / Origin x: 14.8741 Å / Origin y: 17.857 Å / Origin z: -16.7692 Å
111213212223313233
T0.1991 Å20.0546 Å20.0013 Å2-0.1711 Å2-0.0398 Å2--0.1439 Å2
L2.7723 °2-2.0341 °20.2994 °2-2.3573 °2-0.7575 °2--1.9043 °2
S0.1453 Å °-0.0237 Å °-0.0168 Å °-0.2327 Å °-0.0436 Å °0.0137 Å °0.2888 Å °0.2782 Å °-0.0992 Å °
Refinement TLS groupSelection details: all

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