+Open data
-Basic information
Entry | Database: PDB / ID: 2b5e | ||||||
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Title | Crystal Structure of Yeast Protein Disulfide Isomerase | ||||||
Components | Protein disulfide-isomerase | ||||||
Keywords | ISOMERASE / Protein Disulfide Isomerase | ||||||
Function / homology | Function and homology information mannosyl-oligosaccharide 1,2-alpha-mannosidase complex / mannose trimming involved in glycoprotein ERAD pathway / Calnexin/calreticulin cycle / protein alpha-1,2-demannosylation / Insulin processing / protein disulfide-isomerase / positive regulation of endoplasmic reticulum unfolded protein response / protein disulfide isomerase activity / protein-disulfide reductase activity / response to endoplasmic reticulum stress ...mannosyl-oligosaccharide 1,2-alpha-mannosidase complex / mannose trimming involved in glycoprotein ERAD pathway / Calnexin/calreticulin cycle / protein alpha-1,2-demannosylation / Insulin processing / protein disulfide-isomerase / positive regulation of endoplasmic reticulum unfolded protein response / protein disulfide isomerase activity / protein-disulfide reductase activity / response to endoplasmic reticulum stress / unfolded protein binding / protein folding / endoplasmic reticulum lumen / endoplasmic reticulum Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Schindelin, H. / Tian, G. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2006 Title: The crystal structure of yeast protein disulfide isomerase suggests cooperativity between its active sites. Authors: Tian, G. / Xiang, S. / Noiva, R. / Lennarz, W.J. / Schindelin, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2b5e.cif.gz | 107.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2b5e.ent.gz | 86 KB | Display | PDB format |
PDBx/mmJSON format | 2b5e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b5/2b5e ftp://data.pdbj.org/pub/pdb/validation_reports/b5/2b5e | HTTPS FTP |
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-Related structure data
Related structure data | |
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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: 56421.613 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: PDI1, MFP1, TRG1 / Plasmid: pTYB12 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P17967, protein disulfide-isomerase | ||
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#2: Chemical | ChemComp-BA / | ||
#3: Chemical | #4: 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: 2.87 Å3/Da / Density % sol: 57.16 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: sodium cacodylate, magnesium chloride, PEG 2000 MME, barium chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 25, 2005 |
Radiation | Monochromator: 1.1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. obs: 24847 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→20 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.928 / SU B: 17.464 / SU ML: 0.209 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.329 / ESU R Free: 0.246 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 66.965 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.461 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth asym-ID: A / Label asym-ID: A
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