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Yorodumi- PDB-1wv8: Crystal structure of hypothetical protein TTHA1013 from an extrem... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1wv8 | ||||||
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Title | Crystal structure of hypothetical protein TTHA1013 from an extremely thermophilic bacterium thermus thermophilus HB8 | ||||||
Components | hypothetical protein TTHA1013 | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Hypothetical / novel fold / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | TTHA1013-like / Domain of unknown function DUF1902 / Domain of unknown function (DUF1902) / TTHA1013/TTHA0281-like / TTHA1013/TTHA0281-like / 2-Layer Sandwich / Alpha Beta / DUF1902 domain-containing protein Function and homology information | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å | ||||||
Authors | Mizohata, E. / Hattori, M. / Kuramitsu, S. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: Proteins / Year: 2005 Title: Crystal structure of the hypothetical protein TTHA1013 from Thermus thermophilus HB8 Authors: Hattori, M. / Mizohata, E. / Manzoku, M. / Bessho, Y. / Murayama, K. / Terada, T. / Kuramitsu, S. / Shirouzu, M. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1wv8.cif.gz | 22.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1wv8.ent.gz | 17.3 KB | Display | PDB format |
PDBx/mmJSON format | 1wv8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1wv8_validation.pdf.gz | 414.4 KB | Display | wwPDB validaton report |
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Full document | 1wv8_full_validation.pdf.gz | 416.6 KB | Display | |
Data in XML | 1wv8_validation.xml.gz | 5.3 KB | Display | |
Data in CIF | 1wv8_validation.cif.gz | 6.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wv/1wv8 ftp://data.pdbj.org/pub/pdb/validation_reports/wv/1wv8 | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 8013.877 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SJJ5 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.878 Å3/Da / Density % sol: 56 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: ammonium sulfate, sodium acetate, PEG4000, Tris-HCl, Sodium chloride, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.96300, 0.97911, 0.97937, 1.00000 | |||||||||||||||
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Jun 17, 2004 | |||||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.2→50 Å / Num. obs: 5283 / Biso Wilson estimate: 30.3 Å2 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.2→44.95 Å / Rfactor Rfree error: 0.016 / Data cutoff high absF: 573827.92 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 51.5787 Å2 / ksol: 0.355245 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 53.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→44.95 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.055 / Total num. of bins used: 6
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