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Yorodumi- PDB-3ut8: Structural view of a non Pfam singleton and crystal packing analysis -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ut8 | ||||||
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Title | Structural view of a non Pfam singleton and crystal packing analysis | ||||||
Components | Putative uncharacterized protein | ||||||
Keywords | UNKNOWN FUNCTION / a non Pfam singleton / crystal packing analysis / helical fold / ytoplasm | ||||||
Function / homology | Domain of unknown function DUF5071 / Domain of unknown function DUF5071 / Cthe_2751-like superfamily / Domain of unknown function (DUF5071) / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha / IODIDE ION / DUF5071 domain-containing protein Function and homology information | ||||||
Biological species | Clostridium thermocellum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.168 Å | ||||||
Authors | Cheng, C. / Shaw, N. / Zhang, X. / Zhang, M. / Ding, W. / Wang, B.C. / Liu, Z.J. | ||||||
Citation | Journal: Plos One / Year: 2012 Title: Structural view of a non pfam singleton and crystal packing analysis. Authors: Cheng, C. / Shaw, N. / Zhang, X. / Zhang, M. / Ding, W. / Wang, B.C. / Liu, Z.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ut8.cif.gz | 66.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ut8.ent.gz | 49.7 KB | Display | PDB format |
PDBx/mmJSON format | 3ut8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ut/3ut8 ftp://data.pdbj.org/pub/pdb/validation_reports/ut/3ut8 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 15568.289 Da / Num. of mol.: 2 / Mutation: S124Y, T128Y, I129Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium thermocellum (bacteria) / Strain: ATCC 27405 / DSM 1237 / Gene: Cthe_2751 / Production host: Escherichia coli (E. coli) / References: UniProt: A3DJ21 #2: Chemical | ChemComp-IOD / #3: 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: 2.49 Å3/Da / Density % sol: 50.61 % |
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-Data collection
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.541 Å |
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Detector | Date: Feb 22, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.541 Å / Relative weight: 1 |
Reflection | Resolution: 2.168→30.58 Å / Num. obs: 16720 / % possible obs: 97.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 2.17→2.25 Å / % possible all: 97.7 |
-Processing
Software |
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Refinement | Resolution: 2.168→27.148 Å / SU ML: 0.46 / σ(F): 1.34 / Phase error: 20.02 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 25.088 Å2 / ksol: 0.307 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.168→27.148 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: 6
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