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- PDB-1hey: INVESTIGATING THE STRUCTURAL DETERMINANTS OF THE P21-LIKE TRIPHOS... -

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Basic information

Entry
Database: PDB / ID: 1hey
TitleINVESTIGATING THE STRUCTURAL DETERMINANTS OF THE P21-LIKE TRIPHOSPHATE AND MG2+ BINDING SITE
ComponentsCHEY
KeywordsCHEMOTAXIS
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: 2.24 Å
AuthorsBellsolell, L. / Coll, M.
Citation
Journal: J.Mol.Biol. / Year: 1995
Title: Investigating the structural determinants of the p21-like triphosphate and Mg2+ binding site.
Authors: Cronet, P. / Bellsolell, L. / Sander, C. / Coll, M. / Serrano, L.
#1: 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
DepositionApr 7, 1995Processing site: BNL
Revision 1.0Jul 10, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _pdbx_database_status.process_site / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CHEY


Theoretical massNumber of molelcules
Total (without water)13,6041
Polymers13,6041
Non-polymers00
Water1,49583
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.510, 60.510, 129.560
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Atom site foot note1: CIS PROLINE - PRO 110

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Components

#1: Protein CHEY


Mass: 13603.612 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / References: UniProt: P06143, UniProt: P0AE67*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 2.52 Å3/Da / Density % sol: 51.11 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
140 mg/mlprotein1drop
25 mMTris-HCl1drop
330 %(w/v)PEG40001dropprecipitant
40.2 M1dropprecipitantLi2SO4
50.1 MTris-HCl1dropprecipitant

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 0.92
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 11, 1993
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionNum. obs: 6707 / % possible obs: 90.7 % / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.111
Reflection
*PLUS
Highest resolution: 2.24 Å / Num. measured all: 74759 / Rmerge(I) obs: 0.111
Reflection shell
*PLUS
Highest resolution: 2.24 Å / Lowest resolution: 2.36 Å / % possible obs: 84.5 %

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
XDSdata reduction
X-PLORphasing
RefinementResolution: 2.24→8 Å / σ(F): 2
RfactorNum. reflection% reflection
Rwork0.2 --
obs0.2 6494 91.6 %
Displacement parametersBiso mean: 18 Å2
Refinement stepCycle: LAST / Resolution: 2.24→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms948 0 0 83 1031
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
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_deg1.8
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 all: 0.224
Solvent computation
*PLUS
Displacement parameters
*PLUS

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