+Open data
-Basic information
Entry | Database: PDB / ID: 1jat | ||||||
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Title | Mms2/Ubc13 Ubiquitin Conjugating Enzyme Complex | ||||||
Components |
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Keywords | LIGASE / ubiquitin / ubiquitin-conjugating enzyme / E2 / UEV | ||||||
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 / ligase activity ...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 / ligase activity / protein polyubiquitination / ATP binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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 | 1jat.cif.gz | 75.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jat.ent.gz | 56.2 KB | Display | PDB format |
PDBx/mmJSON format | 1jat.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ja/1jat ftp://data.pdbj.org/pub/pdb/validation_reports/ja/1jat | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 17573.998 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: Ubc13 / Plasmid: pGEX / Production host: Escherichia coli (E. coli) / Strain (production host): BL21pJY2 / References: UniProt: P52490, ubiquitin-protein ligase |
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#2: Protein | Mass: 15703.791 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: Mms2 / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21pJY2 / References: UniProt: P53152 |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.81 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG 1000, Tris, pH 7.5, 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: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9115 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 30, 2000 |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9115 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→20 Å / Num. all: 36093 / Num. obs: 36093 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 22.6 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 23 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.359 / % possible all: 97.9 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. measured all: 185078 |
Reflection shell | *PLUS % possible obs: 97.9 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→19.95 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1023636.2 / Data cutoff low absF: 0 / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: flat model / Bsol: 66.7178 Å2 / ksol: 0.423792 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.6→19.95 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.67 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.203 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 28.6 Å2 | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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