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Yorodumi- PDB-4egs: Crystal Structure Analysis of Low Molecular Weight Protein Tyrosi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4egs | ||||||
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Title | Crystal Structure Analysis of Low Molecular Weight Protein Tyrosine Phosphatase from T. tengcongensis | ||||||
Components | Ribose 5-phosphate isomerase RpiB | ||||||
Keywords | ISOMERASE / Tyrosine Phosphatase / Dephosphorylation / HYDROLASE | ||||||
Function / homology | Function and homology information isomerase activity / protein tyrosine phosphatase activity / carbohydrate metabolic process Similarity search - Function | ||||||
Biological species | Thermoanaerobacter tengcongensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Cao, X.F. / Liu, X.Y. / Li, L.F. / Su, X.D. | ||||||
Citation | Journal: To be Published Title: Crystal Structure Analysis of Low Molecular Weight Protein Tyrosine Phosphatase from T. tengcongensis Authors: Cao, X.F. / Liu, X.Y. / Li, L.F. / Su, X.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4egs.cif.gz | 73.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4egs.ent.gz | 54.1 KB | Display | PDB format |
PDBx/mmJSON format | 4egs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eg/4egs ftp://data.pdbj.org/pub/pdb/validation_reports/eg/4egs | HTTPS FTP |
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-Related structure data
Related structure data | 1zggS 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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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 19727.488 Da / Num. of mol.: 2 / Fragment: N-TERMINAL DOMAIN, UNP RESIDUES 1-146 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermoanaerobacter tengcongensis (bacteria) Strain: MB4 / Gene: RpiB, TTE0146 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8RD95 #2: Chemical | #3: Chemical | ChemComp-NA / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.78 Å3/Da / Density % sol: 30.71 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 25% PEG 3350, 0.1M BIS-TRIS, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 11, 2012 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→19.5 Å / Num. obs: 13331 / % possible obs: 98.5 % / Observed criterion σ(I): 3 |
Reflection shell | Resolution: 2.25→2.3 Å / % possible all: 98.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ZGG Resolution: 2.3→19.167 Å / σ(F): 2 / Phase error: 24.03 / Stereochemistry target values: TWIN_LSQ_F
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Solvent computation | Shrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.361 Å2 / ksol: 0.376 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.3→19.167 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9
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