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Yorodumi- PDB-3ong: Crystal structure of UBA2ufd-Ubc9: insights into E1-E2 interactio... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ong | ||||||
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Title | Crystal structure of UBA2ufd-Ubc9: insights into E1-E2 interactions in Sumo pathways | ||||||
Components |
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Keywords | LIGASE | ||||||
Function / homology | Function and homology information SUMO activating enzyme complex / SUMO activating enzyme activity / SUMO conjugating enzyme activity / SUMO is conjugated to E1 (UBA2:SAE1) / SUMOylation of nuclear envelope proteins / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / mitotic spindle elongation / SUMOylation of transcription factors / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of transcription cofactors ...SUMO activating enzyme complex / SUMO activating enzyme activity / SUMO conjugating enzyme activity / SUMO is conjugated to E1 (UBA2:SAE1) / SUMOylation of nuclear envelope proteins / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / mitotic spindle elongation / SUMOylation of transcription factors / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of transcription cofactors / SUMOylation of DNA damage response and repair proteins / SUMOylation of DNA replication proteins / SUMOylation of SUMOylation proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / SUMOylation of RNA binding proteins / Transferases; Acyltransferases; Aminoacyltransferases / SUMO transferase activity / SUMOylation of chromatin organization proteins / protein sumoylation / condensed nuclear chromosome / cell division / ATP binding / nucleus / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 | 3ong.cif.gz | 226.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ong.ent.gz | 186 KB | Display | PDB format |
PDBx/mmJSON format | 3ong.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ong_validation.pdf.gz | 448.8 KB | Display | wwPDB validaton report |
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Full document | 3ong_full_validation.pdf.gz | 454.7 KB | Display | |
Data in XML | 3ong_validation.xml.gz | 20.6 KB | Display | |
Data in CIF | 3ong_validation.cif.gz | 28 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/on/3ong ftp://data.pdbj.org/pub/pdb/validation_reports/on/3ong | HTTPS FTP |
-Related 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: 14324.036 Da / Num. of mol.: 2 / 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 #2: Protein | Mass: 18080.551 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: UBC9, YDL064W / Production host: Escherichia coli (E. coli) References: UniProt: P50623, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) #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: 2.43 Å3/Da / Density % sol: 49.29 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 20% PEG3350, 0.1 M Bis-Tris pH 5.5, 0.2 M Li2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 23, 2008 |
Radiation | Monochromator: 1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 22536 / % possible obs: 94.03 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→38.35 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.925 / SU B: 21.582 / SU ML: 0.232 / Cross valid method: THROUGHOUT / ESU R: 0.568 / ESU R Free: 0.283 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 71.864 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→38.35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.36 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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