+Open data
-Basic information
Entry | Database: PDB / ID: 3bq3 | ||||||
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Title | Crystal structure of S. cerevisiae Dcn1 | ||||||
Components | Defective in cullin neddylation protein 1 | ||||||
Keywords | CELL CYCLE / Ligase / ubiquitin / Nedd8 / neddylation / ubiquitination / SCF / cullin / E3 ligases / E2 / protein degradation | ||||||
Function / homology | Function and homology information ubiquitin-like protein binding / protein neddylation / ubiquitin conjugating enzyme binding / cullin family protein binding / ubiquitin ligase complex / protein-macromolecule adaptor activity Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å | ||||||
Authors | Chou, Y.C. / Sicheri, F. | ||||||
Citation | Journal: Mol.Cell / Year: 2008 Title: Dcn1 Functions as a Scaffold-Type E3 Ligase for Cullin Neddylation. Authors: Kurz, T. / Chou, Y.C. / Willems, A.R. / Meyer-Schaller, N. / Hecht, M.L. / Tyers, M. / Peter, M. / Sicheri, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3bq3.cif.gz | 64 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bq3.ent.gz | 50.7 KB | Display | PDB format |
PDBx/mmJSON format | 3bq3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3bq3_validation.pdf.gz | 438.2 KB | Display | wwPDB validaton report |
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Full document | 3bq3_full_validation.pdf.gz | 440.6 KB | Display | |
Data in XML | 3bq3_validation.xml.gz | 12.4 KB | Display | |
Data in CIF | 3bq3_validation.cif.gz | 17 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bq/3bq3 ftp://data.pdbj.org/pub/pdb/validation_reports/bq/3bq3 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 32497.084 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: DCN1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q12395 |
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#2: Chemical | ChemComp-GOL / |
#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: 2.3 Å3/Da / Density % sol: 46.56 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 400mM Ammonium Acetate, 30% PEG 4000 (w/v), 0.1M Tri-Sodium Citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 8-BM / Wavelength: 0.97914 |
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Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 28, 2005 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97914 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 21992 / % possible obs: 97.6 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 22.28 |
Reflection shell | Resolution: 1.9→1.97 Å / Rmerge(I) obs: 0.479 / Mean I/σ(I) obs: 2.412 / % possible all: 83.7 |
-Processing
Software |
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Refinement | Resolution: 1.9→29.48 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.934 / SU B: 3.975 / SU ML: 0.116 / Cross valid method: THROUGHOUT / ESU R: 0.169 / ESU R Free: 0.157 / 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: 34.15 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→29.48 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.95 Å / Total num. of bins used: 20
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