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- PDB-1v98: Crystal Structure Analysis of Thioredoxin from Thermus thermophilus -
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Open data
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Basic information
Entry | Database: PDB / ID: 1v98 | ||||||
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Title | Crystal Structure Analysis of Thioredoxin from Thermus thermophilus | ||||||
![]() | thioredoxin | ||||||
![]() | OXIDOREDUCTASE / structural genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | ![]() glycerol ether metabolic process / protein-disulfide reductase activity / cell redox homeostasis / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Rehse, P.H. / Tahirov, T.H. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
![]() | ![]() Title: Crystallographic Analysis of Thioredoxin from the Thermophilic Bacteria Thermus thermophilus Authors: Rehse, P.H. / Tahirov, T.H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 56.2 KB | Display | ![]() |
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PDB format | ![]() | 38.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 443.6 KB | Display | ![]() |
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Full document | ![]() | 444.6 KB | Display | |
Data in XML | ![]() | 11.5 KB | Display | |
Data in CIF | ![]() | 15.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1nw2S S: Starting model for refinement |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Details | The biological assembly is a dimer formed through crystallogrphic symmetry. Apply -x,y,-z to both the A and B chains. The A chain requires no unit cell translation, the B chain requires -1 0 1 unit cell translations. |
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Components
#1: Protein | Mass: 15182.782 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q5SI93, thioredoxin-disulfide reductase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 48.98 % |
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Crystal grow | Temperature: 291 K / Method: microbatch / pH: 4.8 Details: Lithium sulfate, Sodium Acetate, pH 4.8, Micro batch, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Detector: CCD / Date: Dec 4, 2003 / Details: mirrors |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.82→56.8 Å / Num. all: 18770 / Num. obs: 18770 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.65 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 16 |
Reflection shell | Resolution: 1.82→1.89 Å / Redundancy: 3.52 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.97 / Num. unique all: 1851 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ID 1NW2 A cahin Resolution: 1.82→56.8 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 29.48 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.82→56.8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.82→1.89 Å
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