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Open data
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Basic information
Entry | Database: PDB / ID: 2dsy | ||||||
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Title | Crystal structure of TTHA0281 from thermus thermophilus HB8 | ||||||
![]() | Hypothetical protein TTHA0281 | ||||||
![]() | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / THERMUS THERMOPHILUS HB8 / HYPOTHETICAL PROTEIN / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Double Stranded RNA Binding Domain - #250 / TTHA1013/TTHA0281-like / Double Stranded RNA Binding Domain / 2-Layer Sandwich / Alpha Beta / Uncharacterized protein![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Okazaki, N. / Kumei, M. / Shinkai, A. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
![]() | ![]() Title: Structure of a UPF0150-family protein from Thermus thermophilus HB8 Authors: Okazaki, N. / Kumei, M. / Manzoku, M. / Kuramitsu, S. / Shirouzu, M. / Shinkai, A. / Yokoyama, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 74.6 KB | Display | ![]() |
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PDB format | ![]() | 60.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 457.8 KB | Display | ![]() |
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Full document | ![]() | 459.5 KB | Display | |
Data in XML | ![]() | 14.7 KB | Display | |
Data in CIF | ![]() | 21.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Details | The biological assembly is tetramer |
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Components
#1: Protein | Mass: 9825.606 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-MG / | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.98 Å3/Da / Density % sol: 37.91 % |
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Crystal grow | Temperature: 291 K / Method: microbatch / pH: 9.37 Details: Protein 7.91mg/mL, PEG4000 17.5w/w(%), CHES-HCl 0.1M, MgCl2 0.05M, pH 9.37, Microbatch, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Mar 1, 2005 / Details: MIRRORS | ||||||||||||
Radiation | Monochromator: BENDING MAGNET / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.89→63.63 Å / Num. all: 24539 / Num. obs: 24539 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 22.72 Å2 / Rmerge(I) obs: 0.068 / Rsym value: 0.043 / Net I/σ(I): 16.1 | ||||||||||||
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.263 / Mean I/σ(I) obs: 4.66 / Num. unique all: 2448 / Rsym value: 0.201 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.43 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.89→1.94 Å / Total num. of bins used: 20
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