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- PDB-2idm: 2.00 A Structure of T87I/Y106W Phosphono-CheY -

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Basic information

Entry
Database: PDB / ID: 2idm
Title2.00 A Structure of T87I/Y106W 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 / thermotaxis / internal peptidyl-lysine acetylation / 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 / thermotaxis / internal peptidyl-lysine acetylation / 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
ACETATE ION / Chemotaxis protein CheY
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 15, 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 ...database_2 / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1572
Polymers14,0981
Non-polymers591
Water1,802100
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.091, 50.544, 52.956
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsBiological assembly is a monomer

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Components

#1: Protein Chemotaxis protein cheY /


Mass: 14098.288 Da / Num. of mol.: 1 / Mutation: D57(CyQ) T87I Y106W
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: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 1.9 Å3/Da / Density % sol: 35.35 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.88
Details: 20% PEG 8000, 0.2M ammonium acetate, 0.1 M MES-NaOH, pH 5.88, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 10, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2→99 Å / Num. obs: 6822 / % possible obs: 88.1 % / Rmerge(I) obs: 0.073 / Χ2: 1.791
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2% possible all
2-2.030.4432351.15562.7
2.03-2.070.3732551.20168.4
2.07-2.110.2793111.40982.1
2.11-2.150.253391.55488.3
2.15-2.20.2683521.60493.4
2.2-2.250.2253421.81392.9
2.25-2.310.1783801.4896
2.31-2.370.2083621.81595.5
2.37-2.440.1613421.74994.7
2.44-2.520.1393781.77696.2
2.52-2.610.1193642.02797.3
2.61-2.710.1143771.75796.4
2.71-2.840.0923682.17397.4
2.84-2.990.083712.23496.1
2.99-3.170.0773772.24995.2
3.17-3.420.0653592.03794.7
3.42-3.760.0563601.95591.4
3.76-4.310.053241.71980.6
4.31-5.430.0482981.4172.7
5.43-990.053281.41873.1

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Processing

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

1c4w


Resolution: 2→20 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.328 378 4.9 %
Rwork0.233 --
obs-6780 88.5 %
Solvent computationBsol: 87.775 Å2
Displacement parametersBiso mean: 48.448 Å2
Baniso -1Baniso -2Baniso -3
1--17.096 Å20 Å20 Å2
2---4.555 Å20 Å2
3---21.652 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1012 0 4 100 1116
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.38126
X-RAY DIFFRACTIONc_bond_d0.014908
LS refinement shellResolution: 2→2.09 Å
RfactorNum. reflection% reflection
Rfree0.328271 378 -
Rwork0.233342 --
obs-6780 88.5 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1newprotein.param
X-RAY DIFFRACTION2CNS_TOPPAR:ion.param
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION4ace.param

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