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Yorodumi- PDB-2yzt: Crystal structure of uncharacterized conserved protein from Therm... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2yzt | ||||||
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Title | Crystal structure of uncharacterized conserved protein from Thermus thermophilus HB8 | ||||||
Components | Putative uncharacterized protein TTHA1756 | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Uncharacterized conserved 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 Function and homology information | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å | ||||||
Authors | Ebihara, A. / Yokoyama, S. / Kuramitsu, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: Proteins / Year: 2008 Title: Crystal structure of uncharacterized protein TTHA1756 from Thermus thermophilus HB8: Structural variety in UPF0150 family proteins. Authors: Ebihara, A. / Manzoku, M. / Iino, H. / Kanagawa, M. / Shinkai, A. / Yokoyama, S. / Kuramitsu, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2yzt.cif.gz | 21.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2yzt.ent.gz | 15.9 KB | Display | PDB format |
PDBx/mmJSON format | 2yzt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2yzt_validation.pdf.gz | 418.1 KB | Display | wwPDB validaton report |
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Full document | 2yzt_full_validation.pdf.gz | 418.1 KB | Display | |
Data in XML | 2yzt_validation.xml.gz | 4.8 KB | Display | |
Data in CIF | 2yzt_validation.cif.gz | 6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yz/2yzt ftp://data.pdbj.org/pub/pdb/validation_reports/yz/2yzt | 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: 7790.551 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: pET-11a / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q5SHH4 |
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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: 2.18 Å3/Da / Density % sol: 43.62 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 0.2M di-Ammonium H citrate, 0.1M Sodium citrate pH5.0, 15% PEG3350, 10MM Phenol, 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: BL26B2 / Wavelength: 0.9789, 0.9000, 0.9794 | ||||||||||||
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Nov 18, 2006 | ||||||||||||
Radiation | Monochromator: SI Double-Crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.8→50 Å / Num. obs: 6606 / % possible obs: 99.9 % / Redundancy: 9.9 % / Biso Wilson estimate: 16.8 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 39.6 | ||||||||||||
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.197 / Mean I/σ(I) obs: 9.2 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.8→43.43 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 809313.02 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 57.9426 Å2 / ksol: 0.378129 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→43.43 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.035 / Total num. of bins used: 6
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Xplor file |
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