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Yorodumi- PDB-1cl0: CRYSTAL STRUCTURE OF REDUCED THIOREDOXIN REDUCTASE FROM ESCHERICH... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1cl0 | ||||||
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Title | CRYSTAL STRUCTURE OF REDUCED THIOREDOXIN REDUCTASE FROM ESCHERICHIA COLI. | ||||||
Components | THIOREDOXIN REDUCTASE | ||||||
Keywords | OXIDOREDUCTASE / FLAVOENZYME | ||||||
Function / homology | Function and homology information thioredoxin-disulfide reductase complex / thioredoxin-disulfide reductase / thioredoxin-disulfide reductase (NADPH) activity / removal of superoxide radicals / cell redox homeostasis / flavin adenine dinucleotide binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Lennon, B.W. / Williams Jr, C.H. / Ludwig, M.L. | ||||||
Citation | Journal: Protein Sci. / Year: 1999 Title: Crystal structure of reduced thioredoxin reductase from Escherichia coli: structural flexibility in the isoalloxazine ring of the flavin adenine dinucleotide cofactor. Authors: Lennon, B.W. / Williams Jr., C.H. / Ludwig, M.L. #1: Journal: J.Mol.Biol. / Year: 1994 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 Jr., C.H. / Kuriyan, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1cl0.cif.gz | 78.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1cl0.ent.gz | 57.3 KB | Display | PDB format |
PDBx/mmJSON format | 1cl0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cl/1cl0 ftp://data.pdbj.org/pub/pdb/validation_reports/cl/1cl0 | HTTPS FTP |
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-Related structure data
Related structure data | 1tdeS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 34529.766 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: FAD AND ACTIVE SITE DISULFIDE (CYS 135 AND CYS 138) REDUCED BY SODIUM DITHIONITE AFTER CRYSTALLIZATION Source: (gene. exp.) Escherichia coli (E. coli) / Description: TRXB-STRAIN / Gene: TRXB / Plasmid: PTRR301 / Cellular location (production host): CYTOPLASM / Gene (production host): TRXB / Production host: Escherichia coli (E. coli) / Strain (production host): A326 / References: UniProt: P0A9P4, 1.6.4.5 |
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#2: Chemical | ChemComp-FAD / |
#3: 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: 2.45 Å3/Da / Density % sol: 50.8 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 8 / Details: pH 8.0 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 25 ℃ / pH: 7 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Mar 1, 1998 / Details: MIRRORS |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→10 Å / Num. obs: 12009 / % possible obs: 96.5 % / Redundancy: 7.8 % / Biso Wilson estimate: 21.1 Å2 / Rsym value: 0.119 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 2.5→2.65 Å / Mean I/σ(I) obs: 2.1 / % possible all: 82.4 |
Reflection | *PLUS Rmerge(I) obs: 0.119 |
Reflection shell | *PLUS % possible obs: 82.4 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1TDE Resolution: 2.5→10 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 Details: BULK SOLVENT MODEL USED DISORDERED REGION (RESIDUES 225-230) WAS MODELED STEREOCHEMICALLY. A HYDROGEN BOND PROBABLY EXISTS BETWEEN THE GAMMA SULFURS OF RESIDUES CYS 135 AND CYS 138.
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Displacement parameters | Biso mean: 24.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.65 Å / Rfactor Rfree error: 0.037 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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