+Open data
-Basic information
Entry | Database: PDB / ID: 3o2u | ||||||
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Title | S. cerevisiae Ubc12 | ||||||
Components | NEDD8-conjugating enzyme UBC12 | ||||||
Keywords | LIGASE / E2 conjugase | ||||||
Function / homology | Function and homology information E2 NEDD8-conjugating enzyme / NEDD8 conjugating enzyme activity / NEDD8 transferase activity / protein neddylation / Neddylation / ATP binding / nucleus Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.003 Å | ||||||
Authors | Scott, D.C. / Monda, J.K. / Grace, C.R.R. / Duda, D.M. / Kriwacki, R.W. / Kurz, T. / Schulman, B.A. | ||||||
Citation | Journal: Mol.Cell / Year: 2010 Title: A dual E3 mechanism for Rub1 ligation to Cdc53. Authors: Scott, D.C. / Monda, J.K. / Grace, C.R. / Duda, D.M. / Kriwacki, R.W. / Kurz, 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 | 3o2u.cif.gz | 88.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3o2u.ent.gz | 66.3 KB | Display | PDB format |
PDBx/mmJSON format | 3o2u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3o2u_validation.pdf.gz | 450.5 KB | Display | wwPDB validaton report |
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Full document | 3o2u_full_validation.pdf.gz | 454.9 KB | Display | |
Data in XML | 3o2u_validation.xml.gz | 17.8 KB | Display | |
Data in CIF | 3o2u_validation.cif.gz | 24.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o2/3o2u ftp://data.pdbj.org/pub/pdb/validation_reports/o2/3o2u | HTTPS FTP |
-Related structure data
Related structure data | 3o2pC 3o6bC 1y8xS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 21372.420 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: UBC12, YLR306W, L2142.3 / Production host: Escherichia coli (E. coli) References: UniProt: P52491, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) #2: Chemical | #3: 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: 2.07 Å3/Da / Density % sol: 40.44 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.6 Details: 27% PEG 3350, 0.1M Tris, 0.2M NaCl, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 29, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. all: 23891 / Num. obs: 23534 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1Y8X, Chain A Resolution: 2.003→25.921 Å / SU ML: 0.22 / σ(F): 0 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.237 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.003→25.921 Å
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Refine LS restraints |
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LS refinement shell |
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