+Open data
-Basic information
Entry | Database: PDB / ID: 2bwf | ||||||
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Title | Crystal structure of the UBL domain of Dsk2 from S. cerevisiae | ||||||
Components | UBIQUITIN-LIKE PROTEIN DSK2 | ||||||
Keywords | SIGNALING PROTEIN / UBIQUITIN / UBA / SIGNALING PROTEINS | ||||||
Function / homology | Function and homology information Cargo recognition for clathrin-mediated endocytosis / spindle pole body duplication / protein localization to vacuole / K48-linked polyubiquitin modification-dependent protein binding / polyubiquitin modification-dependent protein binding / ERAD pathway / protein-macromolecule adaptor activity / ubiquitin-dependent protein catabolic process / nucleus / cytosol Similarity search - Function | ||||||
Biological species | SACCHAROMYCES CEREVISIAE (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å | ||||||
Authors | Lowe, E.D. / Hasan, N. / Trempe, J.-F. / Fonso, L. / Noble, M.E.M. / Endicott, J.A. / Johnson, L.N. / Brown, N.R. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2006 Title: Structures of the Dsk2 Ubl and Uba Domains and Their Complex. Authors: Lowe, E.D. / Hasan, N. / Trempe, J.-F. / Fonso, L. / Noble, M.E.M. / Endicott, J.A. / Johnson, L.N. / Brown, N.R. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2bwf.cif.gz | 76.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2bwf.ent.gz | 57 KB | Display | PDB format |
PDBx/mmJSON format | 2bwf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2bwf_validation.pdf.gz | 423 KB | Display | wwPDB validaton report |
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Full document | 2bwf_full_validation.pdf.gz | 423.7 KB | Display | |
Data in XML | 2bwf_validation.xml.gz | 9.5 KB | Display | |
Data in CIF | 2bwf_validation.cif.gz | 12.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bw/2bwf ftp://data.pdbj.org/pub/pdb/validation_reports/bw/2bwf | HTTPS FTP |
-Related structure data
Related structure data | 2bwbC 2bweC 1bt0S 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 8634.741 Da / Num. of mol.: 2 / Fragment: UBL DOMAIN, RESIDUES 1-75 Source method: isolated from a genetically manipulated source Details: UBIQUITIN-LIKE DOMAIN OF DSK2 PROTEIN Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Plasmid: PGEX-KG / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834(DE3)PLYSS / References: UniProt: P48510 #2: Chemical | #3: Water | ChemComp-HOH / | Sequence details | THE STRUCTURE PRESENTED IS OF THE UBL DOMAIN, RESIDUES 1- 75 OF THE INTACT PROTEIN | |
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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 Å3/Da / Density % sol: 38 % |
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Crystal grow | pH: 7 / Details: pH 7.00 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.933 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Dec 17, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.15→37.8 Å / Num. obs: 48617 / % possible obs: 93.8 % / Observed criterion σ(I): 6 / Redundancy: 4.5 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 3.6 |
Reflection shell | Resolution: 1.15→1.21 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 2.3 / % possible all: 81.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1BT0 Resolution: 1.15→34.92 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.956 / Cross valid method: THROUGHOUT / ESU R: 0.044 / ESU R Free: 0.04 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.83 Å2
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Refinement step | Cycle: LAST / Resolution: 1.15→34.92 Å
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Refine LS restraints |
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