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Open data
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Basic information
Entry | Database: PDB / ID: 1vdc | ||||||
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Title | STRUCTURE OF NADPH DEPENDENT THIOREDOXIN REDUCTASE | ||||||
![]() | NADPH DEPENDENT THIOREDOXIN REDUCTASE | ||||||
![]() | OXIDOREDUCTASE / HYPOTHETICAL PROTEIN / REDOX-ACTIVE CENTER / DISULFIDE OXIDOREDUCTASE / THIOREDOXIN REDUCTASE / FLAVIN ADENINE DINULEOTIDE | ||||||
Function / homology | ![]() thioredoxin-disulfide reductase / thioredoxin-disulfide reductase (NADPH) activity / chloroplast envelope / positive regulation of cell division / removal of superoxide radicals / mitochondrion / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Dai, S. / Eklund, H. | ||||||
![]() | ![]() Title: Crystal structure of Arabidopsis thaliana NADPH dependent thioredoxin reductase at 2.5 A resolution. Authors: Dai, S. / Saarinen, M. / Ramaswamy, S. / Meyer, Y. / Jacquot, J.P. / Eklund, H. #1: ![]() Title: Crystal Structure of Escherichia Coli Thioredoxin Reductase Refined at 2 A Resolution. Implications for a Large Conformational Change During Catalysis Authors: Waksman, G. / Krishna, T.S. / Williams Junior, C.H. / Kuriyan, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 80.4 KB | Display | ![]() |
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PDB format | ![]() | 61.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 724 KB | Display | ![]() |
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Full document | ![]() | 733.3 KB | Display | |
Data in XML | ![]() | 19.5 KB | Display | |
Data in CIF | ![]() | 28.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1trbS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 35420.055 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||
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#2: Chemical | ChemComp-SO4 / | ||
#3: Chemical | ChemComp-FAD / | ||
#4: Water | ChemComp-HOH / | ||
Nonpolymer details | NADPH CAN ALSO BE SEEN WITH LOW OCCUPANCY BUT NO COORDINATESequence details | PROTEIN SEQUENCE NUMBERING IS BASED ON E. COLI NTR SEQUENCE AND IS NOT THE SAME AS THE SEQUENCE ...PROTEIN SEQUENCE NUMBERING IS BASED ON E. COLI NTR SEQUENCE AND IS NOT THE SAME AS THE SEQUENCE NUMBERING IN GENBANK. | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 5.05 Å3/Da / Density % sol: 70.6 % | ||||||||||||||||||
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Crystal grow | Details: 7% ISOPROPANOL (OR 4% MPD) AND 1.8 M AMMONIUM SULFATE | ||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 175 K |
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Diffraction source | Source: ![]() ![]() ![]() ![]() ![]() |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Jul 1, 1995 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.857 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→20 Å / Num. obs: 25745 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 6.81 % / Biso Wilson estimate: 30.92 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 7.7 |
Reflection shell | Resolution: 2.5→2.54 Å / Rmerge(I) obs: 0.487 / % possible all: 100 |
Reflection | *PLUS Num. obs: 20556 / Num. measured all: 139995 |
Reflection shell | *PLUS % possible obs: 100 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1TRB Resolution: 2.5→20 Å / σ(F): 1
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Displacement parameters | Biso mean: 31.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.61 Å
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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