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- PDB-1xkr: X-ray Structure of Thermotoga maritima CheC -

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Basic information

Entry
Database: PDB / ID: 1xkr
TitleX-ray Structure of Thermotoga maritima CheC
Componentschemotaxis protein CheC
KeywordsATTRACTANT / chemotaxis / signal transduction / protein phosphatase
Function / homology
Function and homology information


Hydrolases / chemotaxis / hydrolase activity
Similarity search - Function
: / CheC-like protein / CheC-like family / : / CheC-like / Chemotaxis protein chec / CheC-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / CheY-P phosphatase CheC
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.75 Å
AuthorsPark, S.Y. / Chao, X. / Gonzalez-Bonet, G. / Beel, B.D. / Bilwes, A.M. / Crane, B.R.
CitationJournal: Mol.Cell / Year: 2004
Title: Structure and Function of an Unusual Family of Protein Phosphatases; The Bacterial Chemotaxis Proteins CheC and CheX
Authors: Park, S.Y. / Chao, X. / Gonzalez-Bonet, G. / Beel, B.D. / Bilwes, A.M. / Crane, B.R.
History
DepositionSep 29, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: chemotaxis protein CheC


Theoretical massNumber of molelcules
Total (without water)22,7051
Polymers22,7051
Non-polymers00
Water3,315184
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.3, 66.3, 138.3
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein chemotaxis protein CheC


Mass: 22705.484 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Plasmid: pET28a+ / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: GenBank: 15643666, UniProt: Q9X006*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / 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: 3.37 Å3/Da / Density % sol: 63.5 %
Crystal growTemperature: 298 K / pH: 7.5
Details: Li2SO4, HEPES, aceonitrile, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 7.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.92
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 13, 2004
RadiationMonochromator: SI MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 32043 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.062 / Rsym value: 0.062
Reflection shellResolution: 1.75→1.81 Å / Rmerge(I) obs: 0.368 / Rsym value: 0.368

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
HKL-2000data reduction
RefinementMethod to determine structure: SAD / Resolution: 1.75→50 Å / Isotropic thermal model: ANISOTROPIC / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflectionSelection details
Rfree0.239 5702 RANDOM
Rwork0.226 --
obs0.226 32043 -
all-32043 -
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.37 Å20 Å20 Å2
2---1.37 Å20 Å2
3---2.704 Å2
Refinement stepCycle: LAST / Resolution: 1.75→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1577 0 0 184 1761
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it

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