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- PDB-1c4w: 1.9 A STRUCTURE OF A-THIOPHOSPHONATE MODIFIED CHEY D57C -

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Entry
Database: PDB / ID: 1c4w
Title1.9 A STRUCTURE OF A-THIOPHOSPHONATE MODIFIED CHEY D57C
ComponentsCHEMOTAXIS PROTEIN CHEY
KeywordsSIGNALING PROTEIN / Phosphono-CheY / Active Form of the Response Regulator / Chemotaxis
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 / internal peptidyl-lysine acetylation / thermotaxis / regulation of chemotaxis / bacterial-type flagellum / 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 / internal peptidyl-lysine acetylation / thermotaxis / regulation of chemotaxis / bacterial-type flagellum / phosphorelay response regulator activity / protein acetylation / acetyltransferase activity / phosphorelay signal transduction system / chemotaxis / magnesium ion binding / signal transduction / cytoplasm / cytosol
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 / Chemotaxis protein CheY
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.84 Å
AuthorsHalkides, C.J. / McEvoy, M.M. / Matsumura, P. / Volz, K. / Dahlquist, F.W.
Citation
Journal: Biochemistry / Year: 2000
Title: The 1.9 A resolution crystal structure of phosphono-CheY, an analogue of the active form of the response regulator, CheY.
Authors: Halkides, C.J. / McEvoy, M.M. / Casper, E. / Matsumura, P. / Volz, K. / Dahlquist, F.W.
#1: Journal: Biochemistry / Year: 1998
Title: Synthesis and Biochemical Characterization of an Analogue of CheY-phosphate, a Signal Transduction Protein in Bacterial Chemotaxis
Authors: Halkides, C.J. / Zhu, X. / Phillion, D.P. / Matsumura, P. / Dahlquist, F.W.
#2: Journal: J.Biol.Chem. / Year: 1997
Title: Uncoupled Phosphorylation and Activation in Bacterial Chemotaxis: the 2.3 A Structure of an Aspartate to Lysine Mutant at Position 13 of CheY
Authors: Jiang, M. / Bourret, R.B. / Simon, M.I. / Volz, K.
#3: Journal: J.Biol.Chem. / Year: 1997
Title: Crystal Structures of CheY Mutants Y106W and T87I/Y106W. CheY Activation Correlates with Movement of Residue 106.
Authors: Zhu, X. / Rebello, J. / Matsumura, P. / Volz, K.
#4: Journal: J.Bacteriol. / Year: 1996
Title: Tyrosine 106 Plays an Important Role in Chemotaxis Signal Transduction in Escherichia Coli
Authors: Zhu, X.Y. / Amsler, C.D. / Volz, K. / Matsumura, P.
#5: Journal: J.Biol.Chem. / Year: 1995
Title: Uncoupled Phosphorylation and Activation in Bacterial Chemotaxis. The 2.1 A Structure of a Threonine to Isoleucine Mutant at Position 87 of CheY
Authors: Ganguli, S. / Wang, H. / Matsumura, P. / Volz, K.
History
DepositionSep 28, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Nov 3, 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 1.5Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)14,0631
Polymers14,0631
Non-polymers00
Water2,522140
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.62, 47.74, 53.13
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CHEMOTAXIS PROTEIN CHEY


Mass: 14063.198 Da / Num. of mol.: 1 / Mutation: D57(CYQ)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PRL22 / Production host: Escherichia coli (E. coli) / References: UniProt: P06143, UniProt: P0AE67*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 2.06 Å3/Da / Density % sol: 40.19 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: PEG 6000, SODIUM ACETATE, PIPES, pH 6.9, VAPOR DIFFUSION/HANGING DROP, temperature 298K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
128 %PEG60001reservoir
2200 mMsodium acetate1reservoir
3100 mMPIPES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 10, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.84→50 Å / Num. all: 10492 / Observed criterion σ(I): 1 / Redundancy: 8 % / Rmerge(I) obs: 0.074
Reflection shellResolution: 1.85→1.96 Å / % possible all: 94.1
Reflection
*PLUS
Num. obs: 10492 / Num. measured all: 84092

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Processing

Software
NameClassification
X-PLORmodel building
PROTIN/PROFFTrefinement
MAR345data collection
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
PROTINrefinement
PROFFTrefinement
RefinementResolution: 1.84→10 Å / σ(F): 2
Details: THE ALPHA-THIOPHOSPHONATE GROUP COVALENTLY BOUND TO RESIDUE 57 WAS NOT INCLUDED IN THE REFINEMENT. RESIDUE 57 WAS REFINED AS AN ALANINE.
RfactorNum. reflection% reflection
Rwork0.208 --
all-10403 -
obs-9653 88.3 %
Refinement stepCycle: LAST / Resolution: 1.84→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms991 0 0 140 1131
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.02
X-RAY DIFFRACTIONp_angle_d0.043
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROTIN/PROFFT / Classification: refinement
Refinement
*PLUS
Lowest resolution: 10 Å / σ(F): 2 / Rfactor obs: 0.208
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONp_bond_d0.02
X-RAY DIFFRACTIONp_angle_d0.04
X-RAY DIFFRACTIONp_planar_d0.050.051
X-RAY DIFFRACTIONp_plane_restr0.020.012
X-RAY DIFFRACTIONp_chiral_restr0.150.174
X-RAY DIFFRACTIONp_mcbond_it10.991
X-RAY DIFFRACTIONp_scbond_it11.196
X-RAY DIFFRACTIONp_mcangle_it1.51.614
X-RAY DIFFRACTIONp_scangle_it1.51.959

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