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Yorodumi- PDB-3onh: Crystal structure of UBA2ufd-Ubc9: insights into E1-E2 interactio... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3onh | ||||||
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Title | Crystal structure of UBA2ufd-Ubc9: insights into E1-E2 interactions in Sumo pathways | ||||||
Components | Ubiquitin-activating enzyme E1-like | ||||||
Keywords | LIGASE / SUMO conjugation / Ubc9 | ||||||
Function / homology | Function and homology information SUMO activating enzyme complex / SUMO activating enzyme activity / SUMO is conjugated to E1 (UBA2:SAE1) / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / protein sumoylation / ATP binding / metal ion binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.601 Å | ||||||
Authors | Wang, J. / Taherbhoy, A.M. / Hunt, H.W. / Seyedin, S.N. / Miller, D.W. / Huang, D.T. / Schulman, B.A. | ||||||
Citation | Journal: Plos One / Year: 2010 Title: Crystal structure of UBA2(ufd)-Ubc9: insights into E1-E2 interactions in Sumo pathways. Authors: Wang, J. / Taherbhoy, A.M. / Hunt, H.W. / Seyedin, S.N. / Miller, D.W. / Miller, D.J. / Huang, D.T. / Schulman, B.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3onh.cif.gz | 37.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3onh.ent.gz | 25.5 KB | Display | PDB format |
PDBx/mmJSON format | 3onh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/on/3onh ftp://data.pdbj.org/pub/pdb/validation_reports/on/3onh | HTTPS FTP |
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-Related structure data
Related structure data | 3ongSC 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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Unit cell |
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-Components
#1: Protein | Mass: 14324.036 Da / Num. of mol.: 1 / Fragment: UNP residues 439-563 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: UBA2, PIP2, UAL1, YDR390C, D9509.10 / Production host: Escherichia coli (E. coli) / References: UniProt: P52488 |
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#2: 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: 2.85 Å3/Da / Density % sol: 56.79 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.6 Details: 3M (NH4)2SO4, 1% MPD, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å |
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Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 4, 2010 |
Radiation | Monochromator: KOHZU / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. all: 20193 / Num. obs: 20193 / % possible obs: 94.77 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 1.6→1.66 Å / % possible all: 96.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3ONG Resolution: 1.601→40.096 Å / σ(F): 0.15 / Phase error: 18.96 / Stereochemistry target values: TWIN_LSQ_F
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.878 Å2 / ksol: 0.39 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.601→40.096 Å
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Refine LS restraints |
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LS refinement shell |
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