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- PDB-1udr: CHEY MUTANT WITH LYS 91 REPLACED BY ASP, LYS 92 REPLACED BY ALA, ... -

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Basic information

Entry
Database: PDB / ID: 1udr
TitleCHEY MUTANT WITH LYS 91 REPLACED BY ASP, LYS 92 REPLACED BY ALA, ILE 96 REPLACED BY LYS AND ALA 98 REPLACED BY LEU (STABILIZING MUTATIONS IN HELIX 4)
ComponentsCHEY PROTEIN
KeywordsCHEMOTAXIS / PHOSPHORYL TRANSFER / SIGNAL TRANSDUCTION
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 / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsParraga, A. / Coll, M.
Citation
Journal: J.Mol.Biol. / Year: 2000
Title: Towards understanding a molecular switch mechanism: thermodynamic and crystallographic studies of the signal transduction protein CheY.
Authors: Sola, M. / Lopez-Hernandez, E. / Cronet, P. / Lacroix, E. / Serrano, L. / Coll, M. / Parraga, A.
#1: Journal: J.Mol.Biol. / Year: 1996
Title: The Three-Dimensional Structure of Two Mutants of the Signal Transduction Protein Chey Suggest its Molecular Activation Mechanism
Authors: Bellsolell, L. / Cronet, P. / Majolero, M. / Serrano, L. / Coll, M.
#2: Journal: J.Mol.Biol. / Year: 1994
Title: Magnesium Binding to the Bacterial Chemotaxis Protein Chey Results in Large Conformational Changes Involving its Functional Surface
Authors: Bellsolell, L. / Prieto, J. / Serrano, L. / Coll, M.
History
DepositionNov 5, 1996Processing site: BNL
Revision 1.0Nov 19, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Other
Category: database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details
Revision 1.4Aug 9, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.5May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CHEY PROTEIN
B: CHEY PROTEIN
C: CHEY PROTEIN
D: CHEY PROTEIN


Theoretical massNumber of molelcules
Total (without water)56,7374
Polymers56,7374
Non-polymers00
Water4,035224
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.850, 109.760, 54.000
Angle α, β, γ (deg.)90.00, 111.09, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
CHEY PROTEIN


Mass: 14184.355 Da / Num. of mol.: 4 / Mutation: K91D, K92A, I96K, A98L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: VECTOR PBAT DERIVED FROM PTZ18U (PHARMACIA) / Production host: Escherichia coli (E. coli) / References: UniProt: P06143, UniProt: P0AE67*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.62 Å3/Da / Density % sol: 54 %
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 8.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
13.9 mg/mlprotein1drop
250 mMTris-HCl1drop
31.2 Mammonium sulfate1drop
4100 mMTris-HCl1reservoir
52.4 Mammonium sulfate1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 42474 / % possible obs: 82.9 % / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.058
Reflection
*PLUS
Highest resolution: 1.9 Å / % possible obs: 87.2 % / Observed criterion σ(F): 2 / Rmerge(I) obs: 0.077
Reflection shell
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 1.94 Å / % possible obs: 82.5 %

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
XDSdata reduction
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3CHY

3chy


Resolution: 1.9→8 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.189 -
obs0.189 37665
Refinement stepCycle: LAST / Resolution: 1.9→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4066 0 0 224 4290
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.28
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.222
Solvent computation
*PLUS
Displacement parameters
*PLUS

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