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Yorodumi- PDB-4tve: Structure Of the First Two Thioredoxin Domains of Naumovozyma dai... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4tve | |||||||||
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Title | Structure Of the First Two Thioredoxin Domains of Naumovozyma dairenensis Eps1p | |||||||||
Components | Naumovozyma dairenensis Eps1p | |||||||||
Keywords | ISOMERASE / protein disulfide isomerase / thioredoxin / endoplasmic reticulum / oxidoreductase | |||||||||
Function / homology | Function and homology information protein retention in ER lumen / protein-disulfide reductase (glutathione) activity / : / protein disulfide isomerase activity / unfolded protein binding / membrane => GO:0016020 / endoplasmic reticulum membrane Similarity search - Function | |||||||||
Biological species | Naumovozyma dairenensis (fungus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | |||||||||
Authors | Deborah, F. / 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 | 4tve.cif.gz | 77.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4tve.ent.gz | 55.5 KB | Display | PDB format |
PDBx/mmJSON format | 4tve.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4tve_validation.pdf.gz | 419.3 KB | Display | wwPDB validaton report |
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Full document | 4tve_full_validation.pdf.gz | 420.4 KB | Display | |
Data in XML | 4tve_validation.xml.gz | 15 KB | Display | |
Data in CIF | 4tve_validation.cif.gz | 23 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tv/4tve ftp://data.pdbj.org/pub/pdb/validation_reports/tv/4tve | HTTPS FTP |
-Related structure data
Related structure data | 4tw5C 2b5eS 3t59S C: citing same article (ref.) 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: 31554.703 Da / Num. of mol.: 1 / Fragment: UNP residues 32-294 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Naumovozyma dairenensis (fungus) Strain: ATCC 10597 / BCRC 20456 / CBS 421 / NBRC 0211 / NRRL Y-12639 Gene: NDAI0B01070, NDAI_0B01070 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): Origami B / References: UniProt: G0W5T0, EC: 5.4.3.1 |
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#2: 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: 2.56 Å3/Da / Density % sol: 52.01 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 25% w/v PEG 8,000, 0.1 M MES buffer, pH 6.0, 0.2 M calcium acetate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9763 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 14, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 30298 / % possible obs: 97.79 % / Redundancy: 8.2 % / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 8.1 % / Mean I/σ(I) obs: 2.9 / % possible all: 92.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2B5E, 3T59 Resolution: 1.8→40.181 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.65 / 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: 1.8→40.181 Å
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Refine LS restraints |
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LS refinement shell |
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