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- PDB-3qp6: Crystal structure of CviR (Chromobacterium violaceum 12472) bound... -

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Basic information

Entry
Database: PDB / ID: 3qp6
TitleCrystal structure of CviR (Chromobacterium violaceum 12472) bound to C6-HSL
ComponentsCviR transcriptional regulator
KeywordsTRANSCRIPTION / quorum sensing / agonist / antagonist / LuxR / acylated homoserine lactone / transcription factor / DNA binding protein / ligand binding domain / signal receptor / 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/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
N-[(3S)-2-oxotetrahydrofuran-3-yl]hexanamide / Transcriptional activator, LuxR/UhpA family of regulators
Similarity search - Component
Biological speciesChromobacterium violaceum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 1.2Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.3Sep 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

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Assembly

Deposited unit
A: CviR transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7602
Polymers29,5611
Non-polymers1991
Water4,342241
1
A: CviR transcriptional regulator
hetero molecules

A: CviR transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,5204
Polymers59,1222
Non-polymers3982
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area6570 Å2
ΔGint-33 kcal/mol
Surface area23040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.248, 89.120, 132.125
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-276-

HOH

21A-278-

HOH

31A-282-

HOH

41A-286-

HOH

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Components

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


Mass: 29560.760 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chromobacterium violaceum (bacteria) / Strain: 12472 / Gene: cviR / Plasmid: pET23b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)plyss / References: UniProt: Q7NQP7
#2: Chemical ChemComp-HL6 / N-[(3S)-2-oxotetrahydrofuran-3-yl]hexanamide / N-hexanoyl-L-homoserine lactone


Mass: 199.247 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17NO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 241 / 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: 2.32 Å3/Da / Density % sol: 47.04 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 100 mM imidazole, 10% w/v PEG5000 MME, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.0401
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 6, 2008
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0401 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 20522 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.5 % / Rsym value: 0.071 / Net I/σ(I): 17.127
Reflection shellResolution: 2→2.07 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.319 / Mean I/σ(I) obs: 4.656 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.5_2refinement
PHASERphasing
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3QP7

3qp7
PDB Unreleased entry


Resolution: 2→26.536 Å / SU ML: 0.23 / σ(F): 1.34 / Phase error: 20.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.224 1048 5.12 %
Rwork0.1827 --
obs0.1848 20466 99.89 %
all-20522 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 27.116 Å2 / ksol: 0.323 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.7547 Å2-0 Å20 Å2
2---4.7373 Å2-0 Å2
3---2.9826 Å2
Refinement stepCycle: LAST / Resolution: 2→26.536 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2027 0 14 241 2282
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082085
X-RAY DIFFRACTIONf_angle_d1.0612826
X-RAY DIFFRACTIONf_dihedral_angle_d17.635777
X-RAY DIFFRACTIONf_chiral_restr0.069311
X-RAY DIFFRACTIONf_plane_restr0.004371
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9994-2.10480.26891490.19322711X-RAY DIFFRACTION100
2.1048-2.23660.23981550.17992736X-RAY DIFFRACTION100
2.2366-2.40920.2311500.1852738X-RAY DIFFRACTION100
2.4092-2.65140.23981470.18432755X-RAY DIFFRACTION100
2.6514-3.03460.2181500.1962769X-RAY DIFFRACTION100
3.0346-3.82150.22641480.17912796X-RAY DIFFRACTION100
3.8215-26.5380.19831490.17062913X-RAY DIFFRACTION100

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