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Yorodumi- PDB-2cwy: Crystal structure of conserved hypothetical protein, TTHA0068 fro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2cwy | ||||||
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Title | Crystal structure of conserved hypothetical protein, TTHA0068 from Thermus thermophilus HB8 | ||||||
Components | hypothetical protein TTHA0068 | ||||||
Keywords | Structural Genomics / unknown function / conserved hypothetical protein / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | TTHA0068-like / Protein of unknown function DUF309 / TTHA0068-like superfamily / Domain of unknown function (DUF309) / Hyaluronidase domain-like / Orthogonal Bundle / Mainly Alpha / DUF309 domain-containing protein Function and homology information | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.85 Å | ||||||
Authors | Kishishita, S. / Murayama, K. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Crystal structure of conserved hypothetical protein, TTHA0068 from Thermus thermophilus HB8 Authors: Kishishita, S. / Murayama, K. / 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 | 2cwy.cif.gz | 28.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2cwy.ent.gz | 22 KB | Display | PDB format |
PDBx/mmJSON format | 2cwy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cw/2cwy ftp://data.pdbj.org/pub/pdb/validation_reports/cw/2cwy | 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: 11052.597 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: pET11 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q5SM75 |
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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: 1.8 Å3/Da / Density % sol: 32.6 % |
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Crystal grow | Temperature: 293 K / Method: oil batch / pH: 7.5 Details: PEG8000, Ethylene Glycol, pH 7.5, oil batch, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.979148, 0.979457, 0.964 | ||||||||||||
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: May 27, 2005 / Details: mirrors | ||||||||||||
Radiation | Monochromator: silicon / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.85→50 Å / Num. obs: 7279 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Biso Wilson estimate: 13.3 Å2 / Rsym value: 0.098 / Net I/σ(I): 14.2 | ||||||||||||
Reflection shell | Resolution: 1.85→1.92 Å / Mean I/σ(I) obs: 7.52 / Rsym value: 0.19 / % possible all: 94.3 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.85→32.73 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 497428.66 / 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: 48.0585 Å2 / ksol: 0.362983 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.85→32.73 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.97 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
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Xplor file |
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