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- PDB-3chy: CRYSTAL STRUCTURE OF ESCHERICHIA COLI CHEY REFINED AT 1.7-ANGSTRO... -

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Basic information

Entry
Database: PDB / ID: 3chy
TitleCRYSTAL STRUCTURE OF ESCHERICHIA COLI CHEY REFINED AT 1.7-ANGSTROM RESOLUTION
ComponentsCHEY
KeywordsSIGNAL TRANSDUCTION PROTEIN
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 / protein acetylation / 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 / Chemotaxis protein CheY
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 1.66 Å
AuthorsVolz, K. / Matsumura, P.
CitationJournal: J.Biol.Chem. / Year: 1991
Title: Crystal structure of Escherichia coli CheY refined at 1.7-A resolution.
Authors: Volz, K. / Matsumura, P.
History
DepositionApr 22, 1991Processing site: BNL
Revision 1.0Jan 15, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CHEY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2694
Polymers13,9811
Non-polymers2883
Water2,648147
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.850, 47.030, 54.040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: RESIDUE PRO 110 IS A CIS PROLINE.

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Components

#1: Protein CHEY


Mass: 13981.136 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: CHEY / References: UniProt: P06143, UniProt: P0AE67*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 2.08 Å3/Da / Density % sol: 40.96 %
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: microdialysis / Details: Volz, K., (1986) J.Biol.Chem., 261, 4723. / PH range low: 8.9 / PH range high: 7.4
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12.7 Mammonium salfate11
250 mMTris-HCl11

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Data collection

Reflection
*PLUS
Highest resolution: 1.66 Å / Num. obs: 12108 / Num. measured all: 42197 / Rmerge(I) obs: 0.0406

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Processing

SoftwareName: PROFFT / Classification: refinement
RefinementResolution: 1.66→10 Å
Details: SOLVENT. MOST WATER MOLECULES ARE WELL BEHAVED. A FEW WATERS WITH HIGH TEMPERATURE FACTORS AND CLOSE CONTACTS WITH OTHER WATERS MAY BE PARTIAL SITES. SOLVENT MOLECULE HOH 202 IS PROBABLY AN ...Details: SOLVENT. MOST WATER MOLECULES ARE WELL BEHAVED. A FEW WATERS WITH HIGH TEMPERATURE FACTORS AND CLOSE CONTACTS WITH OTHER WATERS MAY BE PARTIAL SITES. SOLVENT MOLECULE HOH 202 IS PROBABLY AN AMMONIUM ION. MODELLED ATOMS. THE FOLLOWING ATOMS ARE MODELS FOR THE HYPOTHETICAL BINDING POSITIONS OF MG ION AND PHOSPHORYL GROUP TO THE CHEY MOLECULE AND ARE NOT BASED UPON ELECTRON DENSITY: N ASP 57 28.900 2.872 10.690 1.00 10.00 CA ASP 57 27.660 2.298 10.194 1.00 10.00 C ASP 57 26.663 2.175 11.347 1.00 10.00 O ASP 57 27.055 1.915 12.485 1.00 10.00 CB ASP 57 27.891 0.899 9.617 1.00 10.00 CG ASP 57 26.840 0.435 8.608 1.00 10.00 OD1 ASP 57 26.936 0.853 7.123 1.00 10.00 OD2 ASP 57 25.892 -0.286 9.103 1.00 10.00 P PO3 57 27.058 -0.293 6.063 1.00 10.00 O3P PO3 57 27.145 0.067 4.652 1.00 10.00 O2P PO3 57 25.962 -1.249 6.351 1.00 10.00 O4P PO3 57 28.483 -0.924 6.407 1.00 10.00 MG MG 501 27.472 -3.123 8.987 1.00 10.00 ANOTHER POSSIBLE BINDING POSITION FOR THE PHOSPHORYL GROUP IS: N ASP 57 28.900 2.872 10.690 1.00 10.00 CA ASP 57 27.660 2.298 10.194 1.00 10.00 C ASP 57 26.663 2.175 11.347 1.00 10.00 O ASP 57 27.055 1.915 12.485 1.00 10.00 CB ASP 57 27.891 0.899 9.617 1.00 10.00 CG ASP 57 26.840 0.435 8.608 1.00 10.00 OD1 ASP 57 26.936 0.853 7.123 1.00 10.00 OD2 ASP 57 25.892 -0.286 9.103 1.00 10.00 P PO3 57 25.817 0.332 6.159 1.00 10.00 O3P PO3 57 24.535 0.863 6.679 1.00 10.00 O2P PO3 57 25.980 0.539 4.724 1.00 10.00 O4P PO3 57 25.911 -1.249 6.352 1.00 10.00
RfactorNum. reflection
obs0.151 11428
Refinement stepCycle: LAST / Resolution: 1.66→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1003 0 15 147 1165
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0180.02
X-RAY DIFFRACTIONp_angle_d0.0490.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0510.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.9971
X-RAY DIFFRACTIONp_mcangle_it1.5861.5
X-RAY DIFFRACTIONp_scbond_it1.4551
X-RAY DIFFRACTIONp_scangle_it2.4521.5
X-RAY DIFFRACTIONp_plane_restr0.0120.02
X-RAY DIFFRACTIONp_chiral_restr0.160.15
X-RAY DIFFRACTIONp_singtor_nbd0.1860.5
X-RAY DIFFRACTIONp_multtor_nbd0.2020.5
X-RAY DIFFRACTIONp_xhyhbond_nbd0.2240.5
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor2.33
X-RAY DIFFRACTIONp_staggered_tor14.615
X-RAY DIFFRACTIONp_orthonormal_tor22.120
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

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