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- PDB-1u0s: Chemotaxis kinase CheA P2 domain in complex with response regulat... -

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Basic information

Entry
Database: PDB / ID: 1u0s
TitleChemotaxis kinase CheA P2 domain in complex with response regulator CheY from the thermophile thermotoga maritima
Components
  • Chemotaxis protein cheA
  • Chemotaxis protein cheY
KeywordsSIGNALING PROTEIN / protein-protein complex / alpha/beta sandwich / signaling complex / transient interaction / transient complex of thermostable proteins
Function / homology
Function and homology information


archaeal or bacterial-type flagellum-dependent cell motility / histidine kinase / phosphorelay sensor kinase activity / phosphorelay signal transduction system / chemotaxis / protein domain specific binding / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Histidine kinase CheA-like, P2 response regulator-binding domain / : / Chemotaxis protein CheA, P2 response regulator-binding / Chemotaxis protein CheA, P2 response regulator-binding domain superfamily / P2 response regulator binding domain / 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 ...Histidine kinase CheA-like, P2 response regulator-binding domain / : / Chemotaxis protein CheA, P2 response regulator-binding / Chemotaxis protein CheA, P2 response regulator-binding domain superfamily / P2 response regulator binding domain / 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 / 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 CheA / Chemotaxis protein CheY
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsPark, S.Y. / Beel, B.D. / Simon, M.I. / Bilwes, A.M. / Crane, B.R.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2004
Title: In different organisms, the mode of interaction between two signaling proteins is not necessarily conserved
Authors: Park, S.Y. / Beel, B.D. / Simon, M.I. / Bilwes, A.M. / Crane, B.R.
History
DepositionJul 14, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 10, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
Y: Chemotaxis protein cheY
A: Chemotaxis protein cheA


Theoretical massNumber of molelcules
Total (without water)22,9572
Polymers22,9572
Non-polymers00
Water3,639202
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.55, 91.43, 31.66
Angle α, β, γ (deg.)90, 90, 90
Int Tables number18
Space group name H-MP21212
Detailsone CheY-CheA complex per asymmetric unit. One CheY + One CheA P2 constitutes the Biological Assemnbly

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Components

#1: Protein Chemotaxis protein cheY


Mass: 12974.379 Da / Num. of mol.: 1
Fragment: response regulatory domain, CheY response regulator
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: chey / Plasmid: pET28a+ / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q56312
#2: Protein Chemotaxis protein cheA


Mass: 9982.597 Da / Num. of mol.: 1 / Fragment: CheA histidine kinase P2 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: chea / Plasmid: pET28a+ / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q56310, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with a nitrogenous group as acceptor
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / 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: 2.83 Å3/Da / Density % sol: 56.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 25-30% PEG 12K, 0.1M Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 6, 2002
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. all: 135698 / Num. obs: 20993 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 22.7 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 18.9
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 6 % / Rmerge(I) obs: 0.273 / Mean I/σ(I) obs: 3 / Num. unique all: 1028 / % possible all: 99.7

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TMY

4tmy


Resolution: 1.9→30 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.253 1986 -RANDOM
Rwork0.227 ---
all0.23 20209 --
obs0.23 20209 99.7 %-
Displacement parametersBiso mean: 25 Å2
Baniso -1Baniso -2Baniso -3
1--11.157 Å20 Å20 Å2
2--6.111 Å20 Å2
3---5.046 Å2
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1624 0 0 202 1826
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2

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