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- PDB-3qp8: Crystal structure of CviR (Chromobacterium violaceum 12472) ligan... -

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Basic information

Entry
Database: PDB / ID: 3qp8
TitleCrystal structure of CviR (Chromobacterium violaceum 12472) ligand-binding domain bound to C10-HSL
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 receptor / N-decanoyl-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-[(3S)-2-oxotetrahydrofuran-3-yl]decanamide / Transcriptional activator, LuxR/UhpA family of regulators
Similarity search - Component
Biological speciesChromobacterium violaceum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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

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)82,2818
Polymers81,2604
Non-polymers1,0214
Water8,467470
1
A: CviR transcriptional regulator
B: CviR transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1414
Polymers40,6302
Non-polymers5112
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2560 Å2
ΔGint-16 kcal/mol
Surface area16620 Å2
MethodPISA
2
C: CviR transcriptional regulator
D: CviR transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1414
Polymers40,6302
Non-polymers5112
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2870 Å2
ΔGint-14 kcal/mol
Surface area16480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.461, 71.613, 77.737
Angle α, β, γ (deg.)90.00, 114.58, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 20314.945 Da / Num. of mol.: 4 / Fragment: ligand binding domain (UNP residues 8-187)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chromobacterium violaceum (bacteria) / Strain: 12472 / Gene: cviR / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Plyss / References: UniProt: Q7NQP7
#2: Chemical
ChemComp-HL0 / N-[(3S)-2-oxotetrahydrofuran-3-yl]decanamide / N-decanoyl-L-homoserine lactone


Mass: 255.353 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H25NO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 470 / 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: 2.38 Å3/Da / Density % sol: 48.36 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: 100 mM CHES, 1 M sodium citrate, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.0809
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 17, 2008
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0809 Å / Relative weight: 1
ReflectionResolution: 1.6→70.71 Å / Num. obs: 101162 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4 % / Rsym value: 0.043 / Net I/σ(I): 16.678
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.397 / Mean I/σ(I) obs: 2.25 / % possible all: 99.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3QP6

3qp6


Resolution: 1.6→70.71 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.951 / Occupancy max: 1 / Occupancy min: 1 / SU B: 3.879 / SU ML: 0.068 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.095 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2302 5043 5 %RANDOM
Rwork0.1975 95927 --
obs0.1991 100970 99.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 77.59 Å2 / Biso mean: 36.043 Å2 / Biso min: 12.43 Å2
Baniso -1Baniso -2Baniso -3
1--0.56 Å20 Å2-1.67 Å2
2---0.48 Å20 Å2
3----0.35 Å2
Refinement stepCycle: LAST / Resolution: 1.6→70.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5648 0 72 470 6190
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0215834
X-RAY DIFFRACTIONr_angle_refined_deg1.2771.9487883
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6145724
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.36324.377281
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.28215980
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.5081544
X-RAY DIFFRACTIONr_chiral_restr0.080.2850
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024464
X-RAY DIFFRACTIONr_nbd_refined0.2060.22711
X-RAY DIFFRACTIONr_nbtor_refined0.3040.24005
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.130.2406
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2090.283
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1650.229
LS refinement shellResolution: 1.596→1.638 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 397 -
Rwork0.254 6827 -
all-7224 -
obs--96.73 %
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)
11.9792-0.0552-0.09630.8905-0.2231.3292-0.1176-0.07740.13940.04570.0085-0.1684-0.14280.27320.1090.0133-0.00580.0655-0.03530.0115-0.00219.81819.68141.064
21.31110.8260.8421.53150.6231.3818-0.07890.0263-0.0054-0.13190.09480.03070.0956-0.0917-0.0159-0.002-0.01930.106-0.08920.0128-0.0435-15.853.72725.072
31.4337-1.01120.2951.4808-0.58361.33350.0547-0.0187-0.02430.13410.03230.1959-0.3077-0.1476-0.0870.1141-0.04040.1216-0.03260.0504-0.0147-9.56339.6354.511
41.96581.21420.79391.330.56060.6668-0.27970.3087-0.2402-0.29130.3748-0.2789-0.12790.2204-0.09510.065-0.13070.140.0213-0.053-0.021322.47431.1514.509
50.18440.1215-0.2270.1054-0.0550.6331-0.01240.019-0.0375-0.03740.0746-0.0633-0.08210.0459-0.06210.1056-0.00040.1224-0.0162-0.02230.10733.34123.95218.746
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 187
2X-RAY DIFFRACTION2B4 - 187
3X-RAY DIFFRACTION3C7 - 187
4X-RAY DIFFRACTION4D4 - 187
5X-RAY DIFFRACTION5A1
6X-RAY DIFFRACTION5B2
7X-RAY DIFFRACTION5C3
8X-RAY DIFFRACTION5D188

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