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Yorodumi- PDB-5fjw: Yeast delta-COP-I mu-homology domain complexed with Dsl1 WxWx(MSE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5fjw | ||||||
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Title | Yeast delta-COP-I mu-homology domain complexed with Dsl1 WxWx(MSE) peptide | ||||||
Components |
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Keywords | PROTEIN TRANSPORT / COP-I / VESICLE COAT PROTEIN | ||||||
Function / homology | Function and homology information ER-dependent peroxisome organization / RZZ complex / Dsl1/NZR complex / Golgi localization / COPI vesicle coat / COPI-dependent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / mitotic spindle assembly checkpoint signaling / endoplasmic reticulum to Golgi vesicle-mediated transport ...ER-dependent peroxisome organization / RZZ complex / Dsl1/NZR complex / Golgi localization / COPI vesicle coat / COPI-dependent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / mitotic spindle assembly checkpoint signaling / endoplasmic reticulum to Golgi vesicle-mediated transport / protein transport / Golgi membrane / endoplasmic reticulum membrane / endoplasmic reticulum / nucleus / cytosol Similarity search - Function | ||||||
Biological species | SACCHAROMYCES CEREVISIAE (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å | ||||||
Authors | Suckling, R.J. / Evans, P.R. / Owen, D.J. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2015 Title: Structural Basis for the Binding of Tryptophan-Based Motifs by Delta-Cop. Authors: Suckling, R.J. / Poon, P.P. / Travis, S.M. / Majoul, I.V. / Hughson, F.M. / Evans, P.R. / Duden, R. / Owen, D.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5fjw.cif.gz | 436.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fjw.ent.gz | 374.7 KB | Display | PDB format |
PDBx/mmJSON format | 5fjw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fj/5fjw ftp://data.pdbj.org/pub/pdb/validation_reports/fj/5fjw | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 30017.650 Da / Num. of mol.: 8 / Fragment: MU-HOMOLOGY DOMAIN, RESIDUES 288-516 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Gene: RET2, YFR051C / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P43621 #2: Protein/peptide | Mass: 1286.120 Da / Num. of mol.: 8 / Fragment: WXW MOTIF, RESIDUES 411-419 / Source method: obtained synthetically / Details: MSE IN PLACE OF MET / Source: (synth.) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P53847 #3: Water | ChemComp-HOH / | Sequence details | W404 MUTANT SEMET IN PLACE OF MET | |
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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: 3.46 Å3/Da / Density % sol: 64.44 % / Description: NONE |
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Crystal grow | pH: 7 Details: 0.1MHEPES-NA PH 7.0, 0.15M(NH4)2SO4, 21%W/V PEG2250 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97631, 0.97949, 0.97961 | ||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 2, 2011 | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.8→77.6 Å / Num. obs: 80910 / % possible obs: 97.8 % / Observed criterion σ(I): 99 / Redundancy: 7 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 12.9 | ||||||||||||
Reflection shell | Resolution: 2.8→2.85 Å / Redundancy: 7.2 % / Rmerge(I) obs: 1.21 / Mean I/σ(I) obs: 1.1 / % possible all: 97.4 |
-Processing
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Refinement | Method to determine structure: MAD Starting model: NONE Resolution: 2.8→160.67 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.889 / SU B: 17.512 / SU ML: 0.303 / Cross valid method: THROUGHOUT / ESU R: 0.839 / ESU R Free: 0.33 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 87.088 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→160.67 Å
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