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Yorodumi- PDB-3ed3: Crystal Structure of the Yeast Dithiol/Disulfide Oxidoreductase Mpd1p -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ed3 | ||||||
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Title | Crystal Structure of the Yeast Dithiol/Disulfide Oxidoreductase Mpd1p | ||||||
Components | Protein disulfide-isomerase MPD1 | ||||||
Keywords | ISOMERASE / thioredoxin-like domain / CXXC / Endoplasmic reticulum / Glycoprotein / Redox-active center | ||||||
Function / homology | Function and homology information protein-disulfide reductase (glutathione) activity / protein disulfide-isomerase / fungal-type vacuole / protein disulfide isomerase activity / protein-disulfide reductase activity / cell redox homeostasis / protein folding / endoplasmic reticulum lumen / endoplasmic reticulum Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å | ||||||
Authors | Vitu, E. / Greenblatt, H.M. / Fass, D. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 Title: Yeast Mpd1p reveals the structural diversity of the protein disulfide isomerase family Authors: Vitu, E. / Gross, E. / Greenblatt, H.M. / Sevier, C.S. / Kaiser, C.A. / Fass, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ed3.cif.gz | 120.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ed3.ent.gz | 99.3 KB | Display | PDB format |
PDBx/mmJSON format | 3ed3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ed3_validation.pdf.gz | 464.9 KB | Display | wwPDB validaton report |
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Full document | 3ed3_full_validation.pdf.gz | 474.3 KB | Display | |
Data in XML | 3ed3_validation.xml.gz | 25.3 KB | Display | |
Data in CIF | 3ed3_validation.cif.gz | 35.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ed/3ed3 ftp://data.pdbj.org/pub/pdb/validation_reports/ed/3ed3 | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 34229.285 Da / Num. of mol.: 2 / Fragment: UNP residues 23-310 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: MPD1 / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)plysS / References: UniProt: Q12404, protein disulfide-isomerase #2: Chemical | ChemComp-ACT / #3: Chemical | ChemComp-EDO / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.19 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.9 Details: 17% PEG4K, 0.2M sodium acetate, 100mM cacodylic acid (pH5.9), 6-10% ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 2→50 Å / Num. all: 46859 / Num. obs: 45863 / % possible obs: 97.9 % / Redundancy: 5.8 % / Biso Wilson estimate: 51 Å2 / Rsym value: 0.064 / Net I/σ(I): 17 | ||||||||||||||||||
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 5.3 % / Mean I/σ(I) obs: 3.3 / Num. unique all: 4648 / Rsym value: 0.676 / % possible all: 94.7 |
-Processing
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Refinement | Method to determine structure: MAD / Resolution: 2→50 Å / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 2→50 Å
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Refine LS restraints |
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