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- PDB-1eay: CHEY-BINDING (P2) DOMAIN OF CHEA IN COMPLEX WITH CHEY FROM ESCHER... -

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Basic information

Entry
Database: PDB / ID: 1eay
TitleCHEY-BINDING (P2) DOMAIN OF CHEA IN COMPLEX WITH CHEY FROM ESCHERICHIA COLI
Components
  • CHEA
  • CHEY
KeywordsSIGNAL TRANSDUCTION COMPLEX / KINASE / RESPONSE REGULATOR / CHEMOTAXIS
Function / homology
Function and homology information


negative regulation of protein modification process / methyl accepting chemotaxis protein complex / positive regulation of post-translational protein modification / 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 / protein histidine kinase activity / internal peptidyl-lysine acetylation ...negative regulation of protein modification process / methyl accepting chemotaxis protein complex / positive regulation of post-translational protein modification / 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 / protein histidine kinase activity / internal peptidyl-lysine acetylation / thermotaxis / regulation of chemotaxis / bacterial-type flagellum / phosphorelay response regulator activity / protein acetylation / acetyltransferase activity / phosphorelay sensor kinase activity / histidine kinase / phosphorelay signal transduction system / establishment of localization in cell / chemotaxis / magnesium ion binding / signal transduction / ATP binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
CheY-binding domain of CheA / CheY binding / CheY binding / Histidine kinase CheA-like, homodimeric domain / CheY-binding domain of CheA / Histidine kinase CheA-like, homodimeric domain superfamily / Signal transducing histidine kinase, homodimeric domain / Signal transducing histidine kinase, homodimeric domain / : / CheW-like domain profile. ...CheY-binding domain of CheA / CheY binding / CheY binding / Histidine kinase CheA-like, homodimeric domain / CheY-binding domain of CheA / Histidine kinase CheA-like, homodimeric domain superfamily / Signal transducing histidine kinase, homodimeric domain / Signal transducing histidine kinase, homodimeric domain / : / CheW-like domain profile. / CheW-like domain / CheW-like domain superfamily / CheW-like domain / Two component signalling adaptor domain / Histidine Phosphotransfer domain / Hpt domain / Histidine-containing phosphotransfer (HPt) domain profile. / Signal transduction histidine kinase, phosphotransfer (Hpt) domain / HPT domain superfamily / : / Signal transduction histidine kinase-related protein, C-terminal / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Histidine kinase domain / Histidine kinase domain profile. / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Response regulator / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase superfamily / Alpha-Beta Plaits / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chemotaxis protein CheY / Chemotaxis protein CheA / Chemotaxis protein CheY
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR, MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMcevoy, M.M. / Hausrath, A.C. / Randolph, G.B. / Remington, S.J. / Dahlquist, F.W.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1998
Title: Two binding modes reveal flexibility in kinase/response regulator interactions in the bacterial chemotaxis pathway.
Authors: McEvoy, M.M. / Hausrath, A.C. / Randolph, G.B. / Remington, S.J. / Dahlquist, F.W.
History
DepositionApr 23, 1998Processing site: BNL
Revision 1.0Jul 15, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Other / Refinement description
Category: database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4May 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
B: CHEY
C: CHEA
D: CHEA


Theoretical massNumber of molelcules
Total (without water)43,9984
Polymers43,9984
Non-polymers00
Water2,234124
1
A: CHEY
C: CHEA


Theoretical massNumber of molelcules
Total (without water)21,9992
Polymers21,9992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CHEY
D: CHEA


Theoretical massNumber of molelcules
Total (without water)21,9992
Polymers21,9992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.500, 64.200, 158.000
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: 13981.136 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Cellular location: CYTOPLASM / Plasmid: PAR/CHEY / Strain: K38 / References: UniProt: P06143, UniProt: P0AE67*PLUS
#2: Protein CHEA


Mass: 8018.084 Da / Num. of mol.: 2 / Fragment: CHEY-BINDING (P2) DOMAIN / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Cellular location: CYTOPLASM / Plasmid: PP2S / Strain: K38
References: UniProt: P07363, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with a nitrogenous group as acceptor
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.1 Å3/Da / Density % sol: 60 %
Crystal growpH: 7
Details: PROTEIN WAS CRYSTALLIZED FROM .63 M NAH2PO4/1.17 M K2HPO4, 10 MM NH4CL, PH 7.0
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
13.8 mg/mlCheY1drop
22.3 mg/mlP21drop
30.32 Msodium phosphate1drop
40.59 Mpotassium phosphate1drop
55 mM1dropNH4Cl
60.63 Msodium phosphate1reservoir
71.17 Mpotassium phosphate1reservoir
810 mM1reservoirNH4Cl

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 1, 1997
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionHighest resolution: 2 Å / Num. obs: 30701 / % possible obs: 78 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.055
Reflection
*PLUS
Num. measured all: 146840

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Processing

Software
NameVersionClassification
PROTEINmodel building
SIGMAAmodel building
RSSmodel building
TNT5-Frefinement
DENZOdata reduction
SCALEPACKdata scaling
PROTEINphasing
SIGMAAphasing
RSSphasing
RefinementMethod to determine structure: MIR, MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 3CHY AND 1FWP

3chy

1fwp


Resolution: 2→20 Å / Isotropic thermal model: TNT BCORREL V1.0 / σ(F): 0 / Stereochemistry target values: TNT PROTGEO V1.0
RfactorNum. reflection% reflection
Rwork0.217 --
all-30701 -
obs-30701 78 %
Solvent computationSolvent model: BABINET SCALING / Bsol: 150 Å2 / ksol: 0.7 e/Å3
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2934 0 0 124 3058
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.02229661
X-RAY DIFFRACTIONt_angle_deg2.89140042.5
X-RAY DIFFRACTIONt_dihedral_angle_d19.1418200
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.009822
X-RAY DIFFRACTIONt_gen_planes0.0174236
X-RAY DIFFRACTIONt_it4.55329491.5
X-RAY DIFFRACTIONt_nbd0.02710310
Software
*PLUS
Name: TNT / Version: 5-F / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.217
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg19.140
X-RAY DIFFRACTIONt_planar_d0.0092
X-RAY DIFFRACTIONt_plane_restr0.0176

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