[English] 日本語
Yorodumi- PDB-3f3r: Crystal structure of yeast Thioredoxin1-glutathione mixed disulfi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3f3r | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of yeast Thioredoxin1-glutathione mixed disulfide complex | ||||||
Components | Thioredoxin-1 | ||||||
Keywords | ELECTRON TRANSPORT / thioredoxin / glutathione / Deoxyribonucleotide synthesis / Golgi apparatus / Membrane / Nucleus / Protein transport / Redox-active center / Phosphoprotein / Transport | ||||||
Function / homology | Function and homology information membrane fusion priming complex / TP53 Regulates Metabolic Genes / Interconversion of nucleotide di- and triphosphates / The NLRP3 inflammasome / vacuole inheritance / vacuole fusion, non-autophagic / disulfide oxidoreductase activity / Detoxification of Reactive Oxygen Species / fungal-type vacuole / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum ...membrane fusion priming complex / TP53 Regulates Metabolic Genes / Interconversion of nucleotide di- and triphosphates / The NLRP3 inflammasome / vacuole inheritance / vacuole fusion, non-autophagic / disulfide oxidoreductase activity / Detoxification of Reactive Oxygen Species / fungal-type vacuole / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / deoxyribonucleotide biosynthetic process / Oxidative Stress Induced Senescence / protein-disulfide reductase activity / endoplasmic reticulum to Golgi vesicle-mediated transport / cell redox homeostasis / mitochondrial intermembrane space / protein transport / Golgi membrane / mitochondrion / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Zhang, Y.R. / Bao, R. / Zhou, C.Z. / Chen, Y.X. | ||||||
Citation | Journal: Biochim.Biophys.Acta / Year: 2009 Title: Structural and kinetic analysis of Saccharomyces cerevisiae thioredoxin Trx1: implications for the catalytic mechanism of GSSG reduced by the thioredoxin system Authors: Bao, R. / Zhang, Y.R. / Lou, X. / Zhou, C.Z. / Chen, Y.X. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3f3r.cif.gz | 55.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3f3r.ent.gz | 38.7 KB | Display | PDB format |
PDBx/mmJSON format | 3f3r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3f3r_validation.pdf.gz | 945.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3f3r_full_validation.pdf.gz | 964.2 KB | Display | |
Data in XML | 3f3r_validation.xml.gz | 12.8 KB | Display | |
Data in CIF | 3f3r_validation.cif.gz | 16.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f3/3f3r ftp://data.pdbj.org/pub/pdb/validation_reports/f3/3f3r | HTTPS FTP |
-Related structure data
Related structure data | 3f3qC 2fa4S C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||
2 |
| ||||||||||||||||||
3 |
| ||||||||||||||||||
Unit cell |
| ||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 4 / Auth seq-ID: 1 - 103 / Label seq-ID: 7 - 109
|
-Components
#1: Protein | Mass: 12057.748 Da / Num. of mol.: 2 / Mutation: C33S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: TRX1 / Plasmid: p28 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P22217 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.42 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.4 Details: 2.2M Ammonium Sulfate, 0.1M Sodium Acetate, pH 4.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 3, 2008 / Details: mirrors |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→33.31 Å / Num. all: 17174 / Num. obs: 17174 / % possible obs: 92.73 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.9 % / Biso Wilson estimate: 13.7 Å2 / Rmerge(I) obs: 0.033 / Net I/σ(I): 31.9 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.057 / Mean I/σ(I) obs: 22.5 / Num. unique all: 2416 / % possible all: 89.3 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2FA4 Resolution: 1.8→30 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.915 / SU B: 4.762 / SU ML: 0.079 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.165 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 4.19 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→30 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 778 / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
|