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- PDB-2id9: 1.85 A Structure of T87I/Y106W Phosphono-CheY -

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Basic information

Entry
Database: PDB / ID: 2id9
Title1.85 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
Chemotaxis protein CheY
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / 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 1.2May 28, 2014Group: Other
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Oct 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 2.0Jul 26, 2023Group: Advisory / Atomic model / Data collection
Category: atom_site / pdbx_database_remark ...atom_site / pdbx_database_remark / pdbx_validate_symm_contact / pdbx_validate_torsion
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi
Details: Coordinates and associated ncs operations (if present) transformed into standard crystal frame
Provider: repository / Type: Remediation
Revision 2.1Aug 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)14,0981
Polymers14,0981
Non-polymers00
Water1,42379
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: 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 1.97 Å3/Da / Density % sol: 37.69 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.84
Details: 20% PEG 8000, 0.2 M ammonium acetate, 0.1 M MES-NaOH, pH 5.84, 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: Oct 7, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative 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 allΧ2Diffraction-ID% possible all
1.75-1.780.1493211.235157.3
1.78-1.810.1614501.034177.5
1.81-1.850.1425360.879192.6
1.85-1.890.1295600.958196.6
1.89-1.930.125500.851195.5
1.93-1.970.0995640.936198.9
1.97-2.020.0935681.006197.8
2.02-2.070.0825691.043197.6
2.07-2.140.0815681.027199.5
2.14-2.20.0725771.061198.5
2.2-2.280.075811.135198.6
2.28-2.380.0635751.064198.8
2.38-2.480.0615841.07199.3
2.48-2.610.0585901.033199.5
2.61-2.780.0525820.971199.5
2.78-2.990.0516000.949199.8
2.99-3.290.0455870.832199.7
3.29-3.770.0386020.714199.2
3.77-4.750.0346030.635198
4.75-500.0316360.577193.8

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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: 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. atoms985 0 0 79 1064
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.014597
X-RAY DIFFRACTIONc_angle_deg1.4295
LS refinement shellResolution: 1.75→1.93 Å
RfactorNum. reflection% reflection
Rfree0.311793 418 -
Rwork0.24212 --
obs-8281 86.5 %
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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