+Open data
-Basic information
Entry | Database: PDB / ID: 1jbb | ||||||
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Title | Ubiquitin Conjugating Enzyme, Ubc13 | ||||||
Components | ubiquitin conjugating enzyme E2-17.5 KDA | ||||||
Keywords | LIGASE / UBIQUITIN / UBIQUITIN-CONJUGATING ENZYME / E2 | ||||||
Function / homology | Function and homology information protein targeting to vacuolar membrane / Aggrephagy / ubiquitin conjugating enzyme complex / free ubiquitin chain polymerization / fungal-type vacuole membrane / postreplication repair / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / protein K63-linked ubiquitination / protein polyubiquitination ...protein targeting to vacuolar membrane / Aggrephagy / ubiquitin conjugating enzyme complex / free ubiquitin chain polymerization / fungal-type vacuole membrane / postreplication repair / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / protein K63-linked ubiquitination / protein polyubiquitination / ATP binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | VanDemark, A.P. / Hofmann, R.M. / Tsui, C. / Pickart, C.M. / Wolberger, C. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2001 Title: Molecular insights into polyubiquitin chain assembly: crystal structure of the Mms2/Ubc13 heterodimer. Authors: VanDemark, A.P. / Hofmann, R.M. / Tsui, C. / Pickart, C.M. / Wolberger, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jbb.cif.gz | 71.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jbb.ent.gz | 53.9 KB | Display | PDB format |
PDBx/mmJSON format | 1jbb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jb/1jbb ftp://data.pdbj.org/pub/pdb/validation_reports/jb/1jbb | HTTPS FTP |
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-Related structure data
Related structure data | 1jatC 1qcqS S: Starting model for refinement C: citing same article (ref.) |
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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: 17489.984 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Description: GST-fusion / Gene: Ubc13 / Plasmid: pGEX / Production host: Escherichia coli (E. coli) / Strain (production host): BL21pJY2 / References: UniProt: P52490, ubiquitin-protein ligase #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: 2.05 Å3/Da / Density % sol: 39.88 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: PEG 5000-MME, ammonium sulfate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 8 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.542 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 30, 2000 / Details: mirrors |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.542 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. all: 17787 / Num. obs: 17787 / % possible obs: 93.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 20.099 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 27.8 |
Reflection shell | Resolution: 2→2.09 Å / Rmerge(I) obs: 0.223 / Mean I/σ(I) obs: 4.4 / Num. unique all: 1937 / % possible all: 83.2 |
Reflection | *PLUS Lowest resolution: 50 Å / Num. measured all: 55421 |
Reflection shell | *PLUS % possible obs: 83.2 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1QCQ truncated to ALAs Resolution: 2→40 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.09 Å
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 40 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.188 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.268 |