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Yorodumi- PDB-2yzu: Crystal structure of oxidized thioredoxin from Thermus thermophil... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2yzu | ||||||
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Title | Crystal structure of oxidized thioredoxin from Thermus thermophilus HB8 | ||||||
Components | Thioredoxin | ||||||
Keywords | ELECTRON TRANSPORT / Redox protein / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information glycerol ether metabolic process / protein-disulfide reductase activity / cell redox homeostasis Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Ebihara, A. / Yanai, H. / Yokoyama, S. / Kuramitsu, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Crystal structure of oxidized thioredoxin from Thermus thermophilus HB8 Authors: Ebihara, A. / Yanai, H. / 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 | 2yzu.cif.gz | 34 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2yzu.ent.gz | 22 KB | Display | PDB format |
PDBx/mmJSON format | 2yzu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2yzu_validation.pdf.gz | 425.2 KB | Display | wwPDB validaton report |
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Full document | 2yzu_full_validation.pdf.gz | 427.4 KB | Display | |
Data in XML | 2yzu_validation.xml.gz | 6.6 KB | Display | |
Data in CIF | 2yzu_validation.cif.gz | 8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yz/2yzu ftp://data.pdbj.org/pub/pdb/validation_reports/yz/2yzu | HTTPS FTP |
-Related structure data
Related structure data | 2cvkS S: Starting model for refinement |
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Similar structure data | |
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: 12486.024 Da / Num. of mol.: 1 / Fragment: Residues 2-110 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)pLysS / References: UniProt: Q5SHI3 |
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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: 2.04 Å3/Da / Density % sol: 39.76 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.8 Details: 4.3M Sodium chloride, 0.1M HEPES, pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Jul 19, 2005 |
Radiation | Monochromator: SI Double-Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 8643 / % possible obs: 99.7 % / Redundancy: 13.3 % / Biso Wilson estimate: 26.7 Å2 / Rmerge(I) obs: 0.034 / Net I/σ(I): 60.5 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 13.3 % / Rmerge(I) obs: 0.16 / Mean I/σ(I) obs: 17.2 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2CVK Resolution: 1.9→20.9 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1027395.22 / 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: 50.115 Å2 / ksol: 0.398074 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→20.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 6
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Xplor file |
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