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Yorodumi- PDB-8ewx: N-terminal WD40 domain of beta'-COPI subunit with two chains in t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ewx | |||||||||
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Title | N-terminal WD40 domain of beta'-COPI subunit with two chains in the asymmetric unit | |||||||||
Components | Coatomer subunit beta' | |||||||||
Keywords | CYTOSOLIC PROTEIN / COATOMER / TRAFFICKING / SECRETION / ENDOPLASMIC RETICULUM / GOLGI / ER-GOLGI INTERMEDIATE COMPARTMENT / COPI | |||||||||
Function / homology | Function and homology information COPI-coated vesicle membrane / membrane coat / vesicle-mediated transport / intracellular protein transport / Golgi membrane / structural molecule activity Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.24 Å | |||||||||
Authors | Dey, D. / Hasan, S.S. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Protein Expr.Purif. / Year: 2023 Title: Strategies for rapid production of crystallization quality coatomer WD40 domains. Authors: Dey, D. / Hasan, S.S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ewx.cif.gz | 409.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ewx.ent.gz | 305.6 KB | Display | PDB format |
PDBx/mmJSON format | 8ewx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ew/8ewx ftp://data.pdbj.org/pub/pdb/validation_reports/ew/8ewx | HTTPS FTP |
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-Related structure data
Related structure data | 8evlC 8f0eC 4j73S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 34380.730 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Production host: Escherichia coli (E. coli) / References: UniProt: G2WDW6 #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: 2.21 Å3/Da / Density % sol: 44.24 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / Details: PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.92 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 19, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 1.24→29.33 Å / Num. obs: 160014 / % possible obs: 95.1 % / Redundancy: 4.3 % / Biso Wilson estimate: 11.23 Å2 / CC1/2: 0.998 / Net I/σ(I): 10.1 |
Reflection shell | Resolution: 1.24→1.26 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 5385 / CC1/2: 0.572 / % possible all: 64.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4J73 Resolution: 1.24→27.46 Å / SU ML: 0.1025 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.0348 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.49 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.24→27.46 Å
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Refine LS restraints |
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LS refinement shell |
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