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Yorodumi- PDB-2qdl: Crystal structure of scaffolding protein TtCheW from Thermoanaero... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2qdl | ||||||
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Title | Crystal structure of scaffolding protein TtCheW from Thermoanaerobacter tengcongensis | ||||||
Components | Chemotaxis signal transduction protein | ||||||
Keywords | SIGNALING PROTEIN / beta-barrel | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Thermoanaerobacter tengcongensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Yao, W. / Shi, L. / Liang, D.C. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2qdl.cif.gz | 72 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2qdl.ent.gz | 53.9 KB | Display | PDB format |
PDBx/mmJSON format | 2qdl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2qdl_validation.pdf.gz | 452.2 KB | Display | wwPDB validaton report |
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Full document | 2qdl_full_validation.pdf.gz | 457 KB | Display | |
Data in XML | 2qdl_validation.xml.gz | 14.5 KB | Display | |
Data in CIF | 2qdl_validation.cif.gz | 19.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qd/2qdl ftp://data.pdbj.org/pub/pdb/validation_reports/qd/2qdl | HTTPS FTP |
-Related structure data
Related structure data | 2ch4S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Details | The biological assembly is a monomer. |
-Components
#1: 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 | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.48 % |
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Crystal grow | Temperature: 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 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 17, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→19.8 Å / Num. obs: 14589 / % possible obs: 96 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.078 |
Reflection shell | Resolution: 2.2→2.25 Å / Rmerge(I) obs: 0.286 / % possible all: 93.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 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
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.877 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→19.76 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.256 Å / Total num. of bins used: 20
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