+Open data
-Basic information
Entry | Database: PDB / ID: 1z96 | ||||||
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Title | Crystal structure of the Mud1 UBA domain | ||||||
Components | UBA-domain protein mud1 | ||||||
Keywords | PROTEIN TRANSPORT / UBA / ubiquitin / three-helix bundle | ||||||
Function / homology | Function and homology information regulation of exocytosis / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / polyubiquitin modification-dependent protein binding / SNARE binding / protein transport / proteasome-mediated ubiquitin-dependent protein catabolic process / aspartic-type endopeptidase activity / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Schizosaccharomyces pombe (fission yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å | ||||||
Authors | Trempe, J.-F. / Brown, N.R. / Lowe, E.D. / Noble, M.E.M. / Gordon, C. / Campbell, I.D. / Johnson, L.N. / Endicott, J.A. | ||||||
Citation | Journal: Embo J. / Year: 2005 Title: Mechanism of Lys48-linked polyubiquitin chain recognition by the Mud1 UBA domain Authors: Trempe, J.-F. / Brown, N.R. / Lowe, E.D. / Gordon, C. / Campbell, I.D. / Noble, M.E.M. / Endicott, J.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1z96.cif.gz | 40.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1z96.ent.gz | 30.5 KB | Display | PDB format |
PDBx/mmJSON format | 1z96.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z9/1z96 ftp://data.pdbj.org/pub/pdb/validation_reports/z9/1z96 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein/peptide | Mass: 4060.519 Da / Num. of mol.: 2 / Fragment: C-terminal UBA Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast) Gene: mud1 / Plasmid: pGEX-6P1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: UniProt: Q10256 #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: 3.2 Å3/Da / Density % sol: 61 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: sodium formate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 1.8→28.868 Å / Num. all: 10214 / Num. obs: 10214 / % possible obs: 99.79 % / Observed criterion σ(I): 1 / Redundancy: 10.3 % / Biso Wilson estimate: 28.041 Å2 / Rmerge(I) obs: 0.05 / Rsym value: 0.05 / Net I/σ(I): 10.1 | ||||||||||||||||||
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 10.6 % / Rmerge(I) obs: 0.444 / Mean I/σ(I) obs: 1.7 / Num. unique all: 1449 / Rsym value: 0.444 / % possible all: 99.79 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.8→21.89 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.96 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.094 / 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: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.664 Å2
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Refine analyze | Luzzati coordinate error obs: 0.1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→21.89 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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