+Open data
-Basic information
Entry | Database: PDB / ID: 1wd5 | ||||||
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Title | Crystal structure of TT1426 from Thermus thermophilus HB8 | ||||||
Components | hypothetical protein TT1426 | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / hypothetical protein / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å | ||||||
Authors | Shibata, R. / Kukimoto-Niino, M. / Murayama, K. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: Protein Sci. / Year: 2005 Title: Crystal structure of a predicted phosphoribosyltransferase (TT1426) from Thermus thermophilus HB8 at 2.01 A resolution Authors: Kukimoto-Niino, M. / Shibata, R. / Murayama, K. / Hamana, H. / Nishimoto, M. / Bessho, Y. / Terada, T. / Shirouzu, M. / Kuramitsu, S. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1wd5.cif.gz | 53.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1wd5.ent.gz | 41.4 KB | Display | PDB format |
PDBx/mmJSON format | 1wd5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1wd5_validation.pdf.gz | 376.8 KB | Display | wwPDB validaton report |
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Full document | 1wd5_full_validation.pdf.gz | 378.1 KB | Display | |
Data in XML | 1wd5_validation.xml.gz | 5.8 KB | Display | |
Data in CIF | 1wd5_validation.cif.gz | 9.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wd/1wd5 ftp://data.pdbj.org/pub/pdb/validation_reports/wd/1wd5 | 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
#1: Protein | Mass: 22551.406 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SIB2 |
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#2: Chemical | ChemComp-MES / |
#3: 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: 3.1 Å3/Da / Density % sol: 59.8 % |
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-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.97910, 0.97938, 0.97400 | ||||||||||||
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Apr 5, 2004 | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2→50 Å / Num. obs: 31382 / % possible obs: 95.3 % / Observed criterion σ(I): -3 / Redundancy: 7.38 % / Biso Wilson estimate: 6.6 Å2 / Rsym value: 0.107 / Net I/σ(I): 15.37 | ||||||||||||
Reflection shell | Resolution: 2→2.08 Å / Rsym value: 0.303 / % possible all: 67.4 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2→36.76 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 219596.22 / 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: 57.8 Å2 / ksol: 0.36348 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→36.76 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
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Xplor file |
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