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- PDB-4hns: Crystal structure of activated CheY3 of Vibrio cholerae -

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Basic information

Entry
Database: PDB / ID: 4hns
TitleCrystal structure of activated CheY3 of Vibrio cholerae
ComponentsChemotaxis protein CheY
KeywordsSIGNALING PROTEIN / Rossmann fold / Response regulator / kinase / BeF3 and Mg+2 bound
Function / homology
Function and homology information


archaeal or bacterial-type flagellum-dependent cell motility / phosphorelay signal transduction system / metal ion binding / cytoplasm
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
BERYLLIUM TRIFLUORIDE ION / CheY homolog / Chemotaxis protein CheY-3
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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: Chemotaxis protein CheY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1013
Polymers14,0101
Non-polymers902
Water1,928107
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.320, 67.320, 72.660
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Chemotaxis protein CheY / CheY3


Mass: 14010.287 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: VC_2065 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9KQD5, UniProt: Q6BBK8*PLUS
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: BeF3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2.26 Å3/Da / Density % sol: 45.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 10% PEG6000, pH 8.0, 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: May 22, 2012
RadiationMonochromator: Ni filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. all: 7391 / Num. obs: 6881 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 36.6 Å2
Reflection shellHighest resolution: 2.1 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 3TO5

3to5


Resolution: 2.1→24.22 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 1287710.98 / 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
Rfree0.243 351 5.1 %RANDOM
Rwork0.231 ---
obs0.231 6881 95.8 %-
all-7391 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 63.6052 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 56.3 Å2
Baniso -1Baniso -2Baniso -3
1--2.57 Å20 Å20 Å2
2---2.57 Å20 Å2
3---5.14 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.31 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 2.1→24.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms980 0 5 107 1092
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_improper_angle_d1.08
X-RAY DIFFRACTIONc_mcbond_it3.351.5
X-RAY DIFFRACTIONc_mcangle_it5.322
X-RAY DIFFRACTIONc_scbond_it4.322
X-RAY DIFFRACTIONc_scangle_it7.732.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.047 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.357 58 5.2 %
Rwork0.324 1061 -
obs--93.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2cis_peptide.paramwater_rep.top
X-RAY DIFFRACTION3water_rep.paramion.top
X-RAY DIFFRACTION4ion.param

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