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- PDB-1ehc: STRUCTURE OF SIGNAL TRANSDUCTION PROTEIN CHEY -

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Basic information

Entry
Database: PDB / ID: 1ehc
TitleSTRUCTURE OF SIGNAL TRANSDUCTION PROTEIN CHEY
ComponentsCHEY
KeywordsSIGNAL TRANSDUCTION / CHEY / RESPONSE REGULATORS / CHEMOTAXIS / SENSORY TRANSDUCTION / PHOSPHORYLATION / FLAGELLAR ROT
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 / PHASED WITH WT / Resolution: 2.26 Å
AuthorsJiang, M. / Bourret, R. / Simon, M. / Volz, K.
Citation
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.
#1: 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.
#2: 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.
#3: Journal: Biochemistry / Year: 1993
Title: Structural Conservation in the Chey Superfamily
Authors: Volz, K.
#4: Journal: J.Biol.Chem. / Year: 1991
Title: Crystal Structure of Escherichia Coli Chey Refined at 1.7-A Resolution
Authors: Volz, K. / Matsumura, P.
History
DepositionMar 5, 1996Processing site: BNL
Revision 1.0May 15, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 7, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0912
Polymers13,9951
Non-polymers961
Water1,802100
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

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Components

#1: Protein CHEY


Mass: 13995.228 Da / Num. of mol.: 1 / Mutation: D13K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Description: NATURALLY-OCCURRING MUTANT / Plasmid: pRBB40.13DK / Production host: Escherichia coli (E. coli) / References: UniProt: P06143, UniProt: P0AE67*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 2.08 Å3/Da / Density % sol: 40.9 %
Crystal growpH: 8.3 / Details: pH 8.3
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

DiffractionMean temperature: 290 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 2.26 Å / Num. obs: 5108 / % possible obs: 87.8 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.0602
Reflection shellResolution: 2.26→2.37 Å / % possible all: 24.4
Reflection
*PLUS
Num. measured all: 12828

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Processing

Software
NameClassification
PROFFTrefinement
XENGENdata reduction
XENGENdata scaling
RefinementMethod to determine structure: PHASED WITH WT
Starting model: MODIFIED WILD-TYPE CHEY

Resolution: 2.26→10 Å / σ(F): 2
RfactorNum. reflection% reflection
Rwork0.143 --
obs-4432 76.2 %
Displacement parametersBiso mean: 15.6 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 2.26→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms980 0 5 100 1085
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0160.02
X-RAY DIFFRACTIONp_angle_d0.0510.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0570.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.8231
X-RAY DIFFRACTIONp_mcangle_it1.4311.5
X-RAY DIFFRACTIONp_scbond_it0.9161
X-RAY DIFFRACTIONp_scangle_it1.6141.5
X-RAY DIFFRACTIONp_plane_restr0.010.02
X-RAY DIFFRACTIONp_chiral_restr0.1530.15
X-RAY DIFFRACTIONp_singtor_nbd0.2010.5
X-RAY DIFFRACTIONp_multtor_nbd0.2380.5
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.2870.5
X-RAY DIFFRACTIONp_planar_tor1.83
X-RAY DIFFRACTIONp_staggered_tor20.515
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor17.620
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROFFT / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.143
Solvent computation
*PLUS
Displacement parameters
*PLUS

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