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- PDB-4hnr: High resolution structure of Chemotaxis response regulator CheY4 ... -

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Basic information

Entry
Database: PDB / ID: 4hnr
TitleHigh resolution structure of Chemotaxis response regulator CheY4 of Vibrio cholerae
ComponentsChemotaxis protein CheY
KeywordsSIGNALING PROTEIN / Rossmann fold / response regulator protein / kinase
Function / homology
Function and homology information


phosphorelay signal transduction system
Similarity search - Function
: / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Response regulator / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CheY homolog / Chemotaxis protein CheY
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsBiswas, M. / Sen, U. / Dasgupta, J.
CitationJournal: Plos One / Year: 2013
Title: Conformational Barrier of CheY3 and Inability of CheY4 to Bind FliM Control the Flagellar Motor Action in Vibrio cholerae.
Authors: Biswas, M. / Dey, S. / Khamrui, S. / Sen, U. / Dasgupta, J.
History
DepositionOct 21, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2013Group: Database references
Revision 1.2Sep 20, 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

Downloads & links

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Assembly

Deposited unit
A: Chemotaxis protein CheY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4172
Polymers13,3201
Non-polymers961
Water3,027168
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.104, 56.104, 72.283
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Chemotaxis protein CheY / CheY4


Mass: 13320.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: VC_A1096 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9KKK8, UniProt: Q6BBK6*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / 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: 2.47 Å3/Da / Density % sol: 50.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 1.6% AMS, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 20, 2011
RadiationMonochromator: Ni filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. all: 11181 / Num. obs: 10649 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 30.7 Å2
Reflection shellHighest resolution: 1.9 Å

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
AMoREphasing
CNS1.2refinement
AUTOMARdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4H6O

4h6o


Resolution: 1.9→29 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 980743.22 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.2648 533 5 %RANDOM
Rwork0.227 ---
obs0.227 10649 99 %-
all-11181 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 60.5503 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 39.1 Å2
Baniso -1Baniso -2Baniso -3
1-2.98 Å20 Å20 Å2
2--2.98 Å20 Å2
3----5.95 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 1.9→29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms932 0 5 168 1105
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.08
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.691.5
X-RAY DIFFRACTIONc_mcangle_it2.722
X-RAY DIFFRACTIONc_scbond_it2.882
X-RAY DIFFRACTIONc_scangle_it4.492.5
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.042 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.343 66 3.8 %
Rwork0.315 1674 -
obs--99 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4cis_peptide.param

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