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Yorodumi- PDB-2dbs: Crystal structure of a hypothetical protein TTHC002 from Thermus ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2dbs | ||||||
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Title | Crystal structure of a hypothetical protein TTHC002 from Thermus thermophilus HB8 | ||||||
Components | hypothetical protein TTHC002 | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / hypothetical protein / TT2175 / TTHC002 / extremely thermophilic bacteria / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Trna Endonuclease; Chain: A, domain 1 - #20 / TTHC002-like / Trna Endonuclease; Chain: A, domain 1 / 3-Layer(aba) Sandwich / Alpha Beta / Uncharacterized protein Function and homology information | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å | ||||||
Authors | Yoshikawa, S. / Arai, R. / Kamo-Uchikubo, T. / Fusatomi, E. / Akasaka, R. / Bessho, Y. / Murayama, K. / Terada, T. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Crystal structure of a hypothetical protein TTHC002 from Thermus thermophilus HB8 Authors: Yoshikawa, S. / Arai, R. / Kamo-Uchikubo, T. / Fusatomi, E. / Akasaka, R. / Bessho, Y. / Murayama, K. / Terada, T. / 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 | 2dbs.cif.gz | 40.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2dbs.ent.gz | 31.8 KB | Display | PDB format |
PDBx/mmJSON format | 2dbs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2dbs_validation.pdf.gz | 432 KB | Display | wwPDB validaton report |
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Full document | 2dbs_full_validation.pdf.gz | 443.6 KB | Display | |
Data in XML | 2dbs_validation.xml.gz | 10.1 KB | Display | |
Data in CIF | 2dbs_validation.cif.gz | 12.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/db/2dbs ftp://data.pdbj.org/pub/pdb/validation_reports/db/2dbs | 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: 10151.356 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: TTHC002 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)pRARE / References: UniProt: Q5SGN2 #2: 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: 2.11 Å3/Da / Density % sol: 41.59 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.1M HEPES-Na, 1.25M Lithium Sulfate, pH 7.0, 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: 0.97924, 0.97957, 0.96000 | ||||||||||||
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Apr 16, 2005 / Details: Two dimensional focusing mirror | ||||||||||||
Radiation | Monochromator: Si double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2→50 Å / Num. obs: 10858 / % possible obs: 96.8 % / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Biso Wilson estimate: 24 Å2 / Rsym value: 0.073 / Χ2: 1.017 / Net I/σ(I): 13.1 | ||||||||||||
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 3.05 / Num. unique all: 912 / Rsym value: 0.246 / Χ2: 1.011 / % possible all: 80.7 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.1→36 Å / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: THIS IS A TWINNED STRUCTURE. THE TWINNING OPERATOR IS (H,K,L) -> (H,-H-K,-L) AND THE TWINNING FRACTION IS 0.467. THE R-FACTOR IS 0.2561 AND THE R-FREE IS 0.2712 WHEN THIS TWINNING OPERATOR IS USED.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 68.259 Å2 / ksol: 0.354 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.498 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→36 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.2 Å / Total num. of bins used: 8
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Xplor file |
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