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Yorodumi- PDB-4tw5: Structure Of the First Two Thioredoxin Domains of Saccharomyces c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4tw5 | |||||||||
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Title | Structure Of the First Two Thioredoxin Domains of Saccharomyces cerevisiae Eps1p | |||||||||
Components | Eps1p | |||||||||
Keywords | ISOMERASE / protein disulfide isomerase / thioredoxin / endoplasmic reticulum / oxidoreductase | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.37 Å | |||||||||
Authors | Fass, D. / Biran, S. | |||||||||
Funding support | European Union, Israel, 2items
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Citation | Journal: Plos One / Year: 2014 Title: The eps1p protein disulfide isomerase conserves classic thioredoxin superfamily amino Acid motifs but not their functional geometries. Authors: Biran, S. / Gat, Y. / Fass, D. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4tw5.cif.gz | 223.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4tw5.ent.gz | 180.9 KB | Display | PDB format |
PDBx/mmJSON format | 4tw5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tw/4tw5 ftp://data.pdbj.org/pub/pdb/validation_reports/tw/4tw5 | HTTPS FTP |
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-Related 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: 31323.873 Da / Num. of mol.: 4 / Fragment: UNP residues 28-295 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: JAY291 / Gene: EPS1, C1Q_00313 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): Origami B / References: UniProt: C7GJH6, EC: 5.4.3.1 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 53.44 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.4 Details: 24% PEG 4,000, 100 mM sodium acetate, pH 6.4, 25 mM sodium citrate, pH 6.4, 17% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.977 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 1, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.977 Å / Relative weight: 1 |
Reflection | Resolution: 2.37→41.77 Å / Num. obs: 52451 / % possible obs: 99.44 % / Redundancy: 4.9 % / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 2.37→2.45 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 2.9 / % possible all: 99 |
-Processing
Software | Name: PHENIX / Version: (phenix.refine: 1.8.4_1496) / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 2.37→41.767 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.37→41.767 Å
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Refine LS restraints |
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LS refinement shell |
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