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Yorodumi- PDB-2zbw: Crystal structure of thioredoxin reductase-like protein from Ther... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2zbw | ||||||
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Title | Crystal structure of thioredoxin reductase-like protein from Thermus thermophilus HB8 | ||||||
Components | Thioredoxin reductase | ||||||
Keywords | OXIDOREDUCTASE / 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 ferredoxin-NADP+ reductase / ferredoxin-NADP+ reductase activity / NADP binding / flavin adenine dinucleotide binding Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å | ||||||
Authors | Ebihara, A. / Manzoku, M. / Fujimoto, Y. / Kitamura, Y. / Yokoyama, S. / Kuramitsu, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Crystal structure of thioredoxin reductase-like protein from Thermus thermophilus HB8 Authors: Ebihara, A. / Manzoku, M. / Fujimoto, Y. / Kitamura, Y. / 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 | 2zbw.cif.gz | 141.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zbw.ent.gz | 116.7 KB | Display | PDB format |
PDBx/mmJSON format | 2zbw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2zbw_validation.pdf.gz | 949.5 KB | Display | wwPDB validaton report |
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Full document | 2zbw_full_validation.pdf.gz | 958.5 KB | Display | |
Data in XML | 2zbw_validation.xml.gz | 28.4 KB | Display | |
Data in CIF | 2zbw_validation.cif.gz | 40.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zb/2zbw ftp://data.pdbj.org/pub/pdb/validation_reports/zb/2zbw | 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: 36437.984 Da / Num. of mol.: 2 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: Q5SL28, Oxidoreductases; Acting on a sulfur group of donors; With NAD+ or NADP+ as acceptor #2: Chemical | #3: 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: 2.4 Å3/Da / Density % sol: 48.7 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 70MM Bis-Tris pH6.5, 19.6% PEG MME 2000, 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: 0.9791 Å |
Detector | Type: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Nov 17, 2006 |
Radiation | Monochromator: SI Double-Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 42641 / % possible obs: 98.7 % / Redundancy: 11.4 % / Biso Wilson estimate: 23.9 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 39.7 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.095 / Mean I/σ(I) obs: 13.7 / % possible all: 89.3 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.1→50 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 3206975.47 / 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: 45.7236 Å2 / ksol: 0.36128 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
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Xplor file |
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