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- PDB-2qdl: Crystal structure of scaffolding protein TtCheW from Thermoanaero... -

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Basic information

Entry
Database: PDB / ID: 2qdl
TitleCrystal structure of scaffolding protein TtCheW from Thermoanaerobacter tengcongensis
ComponentsChemotaxis signal transduction protein
KeywordsSIGNALING PROTEIN / beta-barrel
Function / homology
Function and homology information


chemotaxis / signal transduction / cytosol
Similarity search - Function
CheA-289, Domain 4 / Chemotaxis protein CheW / CheW-like domain profile. / CheW-like domain / CheW-like domain superfamily / CheW-like domain / Two component signalling adaptor domain / SH3 Domains / SH3 type barrels. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) ...CheA-289, Domain 4 / Chemotaxis protein CheW / CheW-like domain profile. / CheW-like domain / CheW-like domain superfamily / CheW-like domain / Two component signalling adaptor domain / SH3 Domains / SH3 type barrels. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Roll / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chemotaxis signal transduction protein
Similarity search - Component
Biological speciesThermoanaerobacter tengcongensis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsYao, W. / Shi, L. / Liang, D.C.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2007
Title: Crystal structure of scaffolding protein CheW from thermoanaerobacter tengcongensis.
Authors: Yao, W. / Shi, L. / Liang, D.C.
History
DepositionJun 21, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Aug 30, 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 / 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 signal transduction protein
B: Chemotaxis signal transduction protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3865
Polymers37,1092
Non-polymers2763
Water1,856103
1
A: Chemotaxis signal transduction protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8314
Polymers18,5551
Non-polymers2763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Chemotaxis signal transduction protein


Theoretical massNumber of molelcules
Total (without water)18,5551
Polymers18,5551
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.214, 62.235, 55.142
Angle α, β, γ (deg.)90.00, 115.37, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a monomer.

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Components

#1: Protein Chemotaxis signal transduction protein


Mass: 18554.744 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoanaerobacter tengcongensis (bacteria)
Strain: MB4 / Plasmid: pETM10 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8RBV8
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: 0.1M acetate buffer (pH 5.4), 0.2M Sodium Nitrate, 10% (w/v) PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 17, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→19.8 Å / Num. obs: 14589 / % possible obs: 96 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.078
Reflection shellResolution: 2.2→2.25 Å / Rmerge(I) obs: 0.286 / % possible all: 93.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CrystalCleardata collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2CH4

2ch4


Resolution: 2.2→19.76 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.92 / SU B: 5.504 / SU ML: 0.143 / Cross valid method: THROUGHOUT / ESU R: 0.319 / ESU R Free: 0.217 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23278 764 5 %RANDOM
Rwork0.19423 ---
obs0.19619 14589 95.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.877 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20.05 Å2
2--0.1 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.2→19.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2345 0 18 103 2466
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222408
X-RAY DIFFRACTIONr_angle_refined_deg1.451.9963256
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4555298
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.73725.28189
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.94415456
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.572157
X-RAY DIFFRACTIONr_chiral_restr0.0910.2393
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021713
X-RAY DIFFRACTIONr_nbd_refined0.2320.2985
X-RAY DIFFRACTIONr_nbtor_refined0.3180.21651
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.2139
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2260.282
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1240.221
X-RAY DIFFRACTIONr_mcbond_it1.5221.51548
X-RAY DIFFRACTIONr_mcangle_it1.96322471
X-RAY DIFFRACTIONr_scbond_it2.7643936
X-RAY DIFFRACTIONr_scangle_it4.2394.5785
LS refinement shellResolution: 2.2→2.256 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 55 -
Rwork0.221 1017 -
obs--93.62 %

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