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- PDB-5fjz: Yeast delta-COP-I mu-homology domain complexed with Dsl1 WxWxV peptide -
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Open data
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Basic information
Entry | Database: PDB / ID: 5fjz | ||||||
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Title | Yeast delta-COP-I mu-homology domain complexed with Dsl1 WxWxV peptide | ||||||
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![]() | PROTEIN TRANSPORT / COP-I / VESICLE COAT PROTEIN | ||||||
Function / homology | ![]() ER-dependent peroxisome organization / RZZ complex / Dsl1/NZR complex / Golgi localization / COPI-dependent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / COPI vesicle coat / 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-dependent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / COPI vesicle coat / 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Suckling, R.J. / Evans, P.R. / Owen, D.J. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 228 KB | Display | ![]() |
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PDB format | ![]() | 186.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 487.7 KB | Display | ![]() |
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Full document | ![]() | 513.5 KB | Display | |
Data in XML | ![]() | 46.3 KB | Display | |
Data in CIF | ![]() | 66.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5fjwSC ![]() 5fjxC ![]() 5fk0C S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 29783.182 Da / Num. of mol.: 4 / Fragment: MU-HOMOLOGY DOMAIN, RESIDUES 282-546 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() #2: Protein/peptide | Mass: 1207.160 Da / Num. of mol.: 4 / Fragment: WXW MOTIF, RESIDUES 411-419 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 41.95 % / Description: DATA WERE MEROHEDRALLY TWINNED |
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Crystal grow | pH: 6.6 / Details: 0.1 M HEPES PH 6.6, 2.8 M AMMONIUM SULPHATE |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 18, 2011 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.96863 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 1.9→36 Å / Num. obs: 78953 / % possible obs: 98.3 % / Observed criterion σ(I): 99 / Redundancy: 9.1 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 11.3 | |||||||||||||||
Reflection shell | Resolution: 1.9→1.94 Å / Redundancy: 9.2 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 3.4 / % possible all: 98.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 5FJW Resolution: 1.9→36.4 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.019 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.027 / ESU R Free: 0.026 / 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: 28.446 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→36.4 Å
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Refine LS restraints |
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