+Open data
-Basic information
Entry | Database: PDB / ID: 3tdi | ||||||
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Title | yeast Cul1WHB-Dcn1P acetylated Ubc12N complex | ||||||
Components |
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Keywords | Ligase/protein binding / E2:E3 / Ligase-protein binding complex | ||||||
Function / homology | Function and homology information E2 NEDD8-conjugating enzyme / NEDD8 conjugating enzyme activity / ubiquitin-like protein binding / Neddylation / NEDD8 transferase activity / protein neddylation / ubiquitin conjugating enzyme binding / cullin family protein binding / ubiquitin ligase complex / protein-macromolecule adaptor activity ...E2 NEDD8-conjugating enzyme / NEDD8 conjugating enzyme activity / ubiquitin-like protein binding / Neddylation / NEDD8 transferase activity / protein neddylation / ubiquitin conjugating enzyme binding / cullin family protein binding / ubiquitin ligase complex / protein-macromolecule adaptor activity / ATP binding / nucleus Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Scott, D.C. / Monda, J.K. / Bennett, E.J. / Harper, J.W. / Schulman, B.A. | ||||||
Citation | Journal: Science / Year: 2011 Title: N-terminal acetylation acts as an avidity enhancer within an interconnected multiprotein complex. Authors: Scott, D.C. / Monda, J.K. / Bennett, E.J. / Harper, J.W. / 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 | 3tdi.cif.gz | 172 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3tdi.ent.gz | 145.3 KB | Display | PDB format |
PDBx/mmJSON format | 3tdi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/td/3tdi ftp://data.pdbj.org/pub/pdb/validation_reports/td/3tdi | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 24353.648 Da / Num. of mol.: 2 / Fragment: unp residues 70-269 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: DCN1, YLR128W, L3111 / Plasmid: pGEX / Production host: Escherichia coli (E. coli) / References: UniProt: Q12395 #2: Protein/peptide | Mass: 2902.372 Da / Num. of mol.: 2 / Fragment: unp residues 2-24 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: L2142.3, UBC12, YLR306W / Plasmid: pGEX / Production host: Escherichia coli (E. coli) References: UniProt: P52491, 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: 2.37 Å3/Da / Density % sol: 48.03 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.9 Details: 20% PEG3350, 0.1M Bis-Tris Propane, 0.2M Na/K tartrate, pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 77 K | ||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.91917 Å | ||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 16, 2010 | ||||||||||||||||||
Radiation | Monochromator: Cryogenically-cooled single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength | Wavelength: 0.91917 Å / Relative weight: 1 | ||||||||||||||||||
Reflection | Resolution: 2.3→40 Å / Num. obs: 21323 / % possible obs: 96.1 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 2.8 / Rmerge(I) obs: 0.123 / Rsym value: 0.123 / Net I/σ(I): 13.5 | ||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→37 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.891 / SU B: 12.819 / SU ML: 0.176 / Cross valid method: THROUGHOUT / ESU R Free: 0.281 / 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: 31.054 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→37 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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