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- PDB-3qp1: Crystal structure of CviR ligand-binding domain bound to the nati... -

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Basic information

Entry
Database: PDB / ID: 3qp1
TitleCrystal structure of CviR ligand-binding domain bound to the native ligand C6-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


quorum sensing / 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]hexanamide / CviR transcriptional regulator
Similarity search - Component
Biological speciesChromobacterium violaceum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 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)20,5802
Polymers20,3811
Non-polymers1991
Water2,108117
1
A: CviR transcriptional regulator
hetero molecules

A: CviR transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1614
Polymers40,7622
Non-polymers3982
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area2210 Å2
ΔGint-16 kcal/mol
Surface area16510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.543, 55.973, 125.223
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-189-

HOH

21A-195-

HOH

31A-294-

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-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.: 117 / 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: 48.48 %
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: Jun 5, 2010
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: 1.55→62.622 Å / Num. all: 28892 / Num. obs: 28173 / % possible obs: 96 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 11 % / Rsym value: 0.046
Reflection shellResolution: 1.55→1.61 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.476 / Mean I/σ(I) obs: 2.536 / % possible all: 96

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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: 1.55→62.62 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.94 / SU B: 3.709 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.094 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24735 1423 5.1 %RANDOM
Rwork0.21519 ---
all0.21681 28173 --
obs0.21681 26749 97.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.393 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20 Å20 Å2
2--0.51 Å20 Å2
3----0.72 Å2
Refinement stepCycle: LAST / Resolution: 1.55→62.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1403 0 14 117 1534
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0211445
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2341.9551955
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5665177
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.67124.02872
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.93515247
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.0021513
X-RAY DIFFRACTIONr_chiral_restr0.0810.2212
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021109
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2110.2654
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.2996
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.2135
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2370.232
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2670.216
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0341.5910
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.66621416
X-RAY DIFFRACTIONr_scbond_it2.2793600
X-RAY DIFFRACTIONr_scangle_it3.5674.5539
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.548→1.588 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 108 -
Rwork0.259 1832 -
obs--93.05 %
Refinement TLS params.Method: refined / Origin x: 14.8583 Å / Origin y: 18.0624 Å / Origin z: 45.6779 Å
111213212223313233
T0.0056 Å20.0505 Å2-0.0035 Å2--0.0143 Å2-0.0318 Å2---0.0259 Å2
L1.0485 °2-0.7966 °20.3016 °2-0.6363 °2-0.3742 °2--0.7635 °2
S0.1007 Å °0.0035 Å °0.0187 Å °-0.1261 Å °-0.0428 Å °0.0356 Å °0.1506 Å °0.1048 Å °-0.0579 Å °

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