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- PDB-6a51: Novel Regulators CheP and CheQ Specifically Control Chemotaxis Co... -

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Basic information

Entry
Database: PDB / ID: 6a51
TitleNovel Regulators CheP and CheQ Specifically Control Chemotaxis Core Gene cheVAW Transcription in Bacterial Pathogen Campylobacter jejuni
ComponentsCheQ
KeywordsUNKNOWN FUNCTION / chemotaxis / gene regulation / Campylobacter / HDOD domain
Function / homologyUncharacterized protein / Cysteine permease
Function and homology information
Biological speciesCampylobacter jejuni subsp. jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsLu, G. / Gao, B. / Cha, G. / Chen, Z. / Mo, R.
Funding support China, 1items
OrganizationGrant numberCountry
China
CitationJournal: Mol.Microbiol. / Year: 2019
Title: The novel regulators CheP and CheQ control the core chemotaxis operon cheVAW in Campylobacter jejuni.
Authors: Cha, G. / Chen, Z. / Mo, R. / Lu, G. / Gao, B.
History
DepositionJun 21, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CheQ
B: CheQ


Theoretical massNumber of molelcules
Total (without water)39,7702
Polymers39,7702
Non-polymers00
Water2,378132
1
A: CheQ


Theoretical massNumber of molelcules
Total (without water)19,8851
Polymers19,8851
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CheQ


Theoretical massNumber of molelcules
Total (without water)19,8851
Polymers19,8851
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1980 Å2
ΔGint-8 kcal/mol
Surface area16050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.043, 109.043, 107.303
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein CheQ / Cysteine permease


Mass: 19885.064 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni subsp. jejuni (Campylobacter)
Gene: CjjRM3196_0237, CV369_00065
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A0E1ERD4, UniProt: Q0PBQ6*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 4.32 Å3/Da / Density % sol: 71.54 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.1 M BIS-TRIS pH 5.5, 3.0 M Sodium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97776 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97776 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 20493 / % possible obs: 99.9 % / Redundancy: 17 % / Rmerge(I) obs: 0.155 / Net I/σ(I): 21.692
Reflection shellResolution: 2.6→2.69 Å / Rmerge(I) obs: 0.808 / Num. unique obs: 1946 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: SAD / Resolution: 2.6→50 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / Phase error: 22.84
RfactorNum. reflection% reflection
Rfree0.2281 972 4.76 %
Rwork0.1843 --
obs0.1864 20418 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2604 0 0 132 2736
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092680
X-RAY DIFFRACTIONf_angle_d1.0443606
X-RAY DIFFRACTIONf_dihedral_angle_d15.6091580
X-RAY DIFFRACTIONf_chiral_restr0.059375
X-RAY DIFFRACTIONf_plane_restr0.006453
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6001-2.73720.32041420.25512664X-RAY DIFFRACTION98
2.7372-2.90860.29661510.24412708X-RAY DIFFRACTION100
2.9086-3.13320.30821410.24092747X-RAY DIFFRACTION100
3.1332-3.44840.23781060.19812777X-RAY DIFFRACTION100
3.4484-3.94720.18731460.17242771X-RAY DIFFRACTION100
3.9472-4.97230.19371570.13782805X-RAY DIFFRACTION100
4.9723-48.77410.20691290.17232974X-RAY DIFFRACTION100

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