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- PDB-1squ: Structural Genomics, Crystal structure of the CheX protein from T... -

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Basic information

Entry
Database: PDB / ID: 1squ
TitleStructural Genomics, Crystal structure of the CheX protein from Thermotoga maritima
ComponentsCheX protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Alpha-beta sandwich / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


Hydrolases / chemotaxis / hydrolase activity
Similarity search - Function
CheC-like family / CheY-P phosphatase CheX-like / Chemotaxis phosphatase CheX-like domain / Chemotaxis phosphatase CheX / CheC-like / Chemotaxis protein chec / CheC-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CheY-P phosphatase CheX
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å
AuthorsZhang, R. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of the protein CheX from Thermotoga maritima
Authors: Zhang, R. / Savchenko, A. / Edwards, A. / Joachimiak, A.
History
DepositionMar 19, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 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 / database_2
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
A: CheX protein
B: CheX protein


Theoretical massNumber of molelcules
Total (without water)32,9342
Polymers32,9342
Non-polymers00
Water905
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2460 Å2
ΔGint-15 kcal/mol
Surface area13240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.241, 73.031, 78.341
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThis protein existed as dimer. MolA and MolB represent the dimer in the asymmtric unit.

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Components

#1: Protein CheX protein /


Mass: 16467.086 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9X1V3
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 2.4 Å3/Da / Density % sol: 48.71 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20% PEG 3350, 10% isopropanol, 0.1M sodium Cacodylate, 15% MPD, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9795, 0.9797, 0.94656
DetectorType: SBC-2 / Detector: CCD / Date: Mar 2, 2003 / Details: mirrors
RadiationMonochromator: Si 111 Channel / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.97971
30.946561
ReflectionResolution: 2.38→50 Å / Num. all: 13192 / Num. obs: 12325 / % possible obs: 93.43 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 4 / Redundancy: 6 % / Biso Wilson estimate: 42 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 31.7
Reflection shellResolution: 2.38→2.48 Å / Redundancy: 5 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 2.33 / Num. unique all: 1311 / % possible all: 91.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
SBC-Collectdata collection
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.4→45.15 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 392722.49 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: The number of reflections used in the refinement included Friedel pairs
RfactorNum. reflection% reflectionSelection details
Rfree0.32 1033 4.8 %RANDOM
Rwork0.239 ---
obs0.239 21448 89.5 %-
all-23964 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.573 Å2 / ksol: 0.295503 e/Å3
Displacement parametersBiso mean: 54.7 Å2
Baniso -1Baniso -2Baniso -3
1--2.28 Å20 Å20 Å2
2---3.13 Å20 Å2
3---5.41 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.51 Å0.41 Å
Luzzati d res low-5 Å
Luzzati sigma a0.54 Å0.58 Å
Refinement stepCycle: LAST / Resolution: 2.4→45.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2286 0 0 5 2291
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d24.5
X-RAY DIFFRACTIONc_improper_angle_d0.9
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.406 161 5.1 %
Rwork0.367 3008 -
obs--79.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3ION.PARAM

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