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- PDB-2id7: 1.75 A Structure of T87I Phosphono-CheY -

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Basic information

Entry
Database: PDB / ID: 2id7
Title1.75 A Structure of T87I Phosphono-CheY
ComponentsChemotaxis protein cheY
KeywordsSIGNALING PROTEIN / alpha beta protein Flavodoxin-like topology Rossman fold
Function / homology
Function and homology information


bacterial-type flagellum basal body, C ring / bacterial-type flagellum rotor complex / bacterial-type flagellum-dependent swimming motility / regulation of bacterial-type flagellum-dependent cell motility / aerotaxis / bacterial-type flagellum / regulation of chemotaxis / internal peptidyl-lysine acetylation / thermotaxis / phosphorelay response regulator activity ...bacterial-type flagellum basal body, C ring / bacterial-type flagellum rotor complex / bacterial-type flagellum-dependent swimming motility / regulation of bacterial-type flagellum-dependent cell motility / aerotaxis / bacterial-type flagellum / regulation of chemotaxis / internal peptidyl-lysine acetylation / thermotaxis / phosphorelay response regulator activity / acetyltransferase activity / phosphorelay signal transduction system / chemotaxis / magnesium ion binding / signal transduction / cytosol / 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
Chemotaxis protein CheY
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsHalkides, C.J. / Haas, R.M. / McAdams, K.A. / Casper, E.S. / Santarsiero, B.D. / Mesecar, A.D.
CitationJournal: Arch.Biochem.Biophys. / Year: 2008
Title: The structures of T87I phosphono-CheY and T87I/Y106W phosphono-CheY help to explain their binding affinities to the FliM and CheZ peptides.
Authors: McAdams, K. / Casper, E.S. / Matthew Haas, R. / Santarsiero, B.D. / Eggler, A.L. / Mesecar, A. / Halkides, C.J.
History
DepositionSep 14, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chemotaxis protein cheY


Theoretical massNumber of molelcules
Total (without water)14,0751
Polymers14,0751
Non-polymers00
Water2,090116
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.350, 49.960, 53.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a monomer

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Components

#1: Protein Chemotaxis protein cheY


Mass: 14075.252 Da / Num. of mol.: 1 / Mutation: D57(CyQ) T87I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: cheY / Production host: Escherichia coli (E. coli) / Strain (production host): B834 DE3 / References: UniProt: P0AE67
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 1.98 Å3/Da / Density % sol: 37.79 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 28% PEG 3200, 0.2M ammonium chloride, 0.1M sodium acetate, pH 4.60, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Feb 20, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 11203 / % possible obs: 95 % / Rmerge(I) obs: 0.047 / Χ2: 0.934
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2% possible all
1.75-1.780.1493211.23557.3
1.78-1.810.1614501.03477.5
1.81-1.850.1425360.87992.6
1.85-1.890.1295600.95896.6
1.89-1.930.125500.85195.5
1.93-1.970.0995640.93698.9
1.97-2.020.0935681.00697.8
2.02-2.070.0825691.04397.6
2.07-2.140.0815681.02799.5
2.14-2.20.0725771.06198.5
2.2-2.280.075811.13598.6
2.28-2.380.0635751.06498.8
2.38-2.480.0615841.0799.3
2.48-2.610.0585901.03399.5
2.61-2.780.0525820.97199.5
2.78-2.990.0516000.94999.8
2.99-3.290.0455870.83299.7
3.29-3.770.0386020.71499.2
3.77-4.750.0346030.63598
4.75-500.0316360.57793.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT1.701data extraction
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1C4W

1c4w


Resolution: 1.75→20 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.202 569 4.8 %
Rwork0.17 --
obs-10988 93.7 %
Solvent computationBsol: 50.912 Å2
Displacement parametersBiso mean: 19.724 Å2
Baniso -1Baniso -2Baniso -3
1-0.077 Å20 Å20 Å2
2---0.28 Å20 Å2
3---0.203 Å2
Refinement stepCycle: LAST / Resolution: 1.75→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1033 0 0 116 1149
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_bond_d0.018
LS refinement shellResolution: 1.75→1.81 Å
RfactorNum. reflection% reflection
Rfree0.201786 569 -
Rwork0.170202 --
obs-10988 93.7 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1newprotein.param
X-RAY DIFFRACTION2CNS_TOPPAR:ion.param
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.param

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