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Yorodumi- PDB-1zuo: Structure of Human Ubiquitin-Conjugating Enzyme (UBCi) Involved i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1zuo | ||||||
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Title | Structure of Human Ubiquitin-Conjugating Enzyme (UBCi) Involved in Embryo Attachment and Implantation | ||||||
Components | Hypothetical protein LOC92912 | ||||||
Keywords | LIGASE / UBIQUITIN-CONJUGATING ENZYME / STRUCTURAL GENOMICS CONSORTIUM / SGC | ||||||
Function / homology | Function and homology information E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / protein K48-linked ubiquitination / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / protein polyubiquitination / ubiquitin-protein transferase activity / Antigen processing: Ubiquitination & Proteasome degradation / protein ubiquitination / ATP binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å | ||||||
Authors | Walker, J.R. / Avvakumov, G.V. / Cui, H. / Newman, E.M. / Mackenzie, F. / Sundstrom, M. / Arrowsmith, C. / Edwards, A. / Bochkarev, A. / Dhe-Paganon, S. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: Mol Cell Proteomics / Year: 2012 Title: A human ubiquitin conjugating enzyme (E2)-HECT E3 ligase structure-function screen. Authors: Sheng, Y. / Hong, J.H. / Doherty, R. / Srikumar, T. / Shloush, J. / Avvakumov, G.V. / Walker, J.R. / Xue, S. / Neculai, D. / Wan, J.W. / Kim, S.K. / Arrowsmith, C.H. / Raught, B. / Dhe-Paganon, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1zuo.cif.gz | 73.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1zuo.ent.gz | 59.8 KB | Display | PDB format |
PDBx/mmJSON format | 1zuo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1zuo_validation.pdf.gz | 452.2 KB | Display | wwPDB validaton report |
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Full document | 1zuo_full_validation.pdf.gz | 454 KB | Display | |
Data in XML | 1zuo_validation.xml.gz | 15.8 KB | Display | |
Data in CIF | 1zuo_validation.cif.gz | 22.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zu/1zuo ftp://data.pdbj.org/pub/pdb/validation_reports/zu/1zuo | HTTPS FTP |
-Related structure data
Related structure data | 1y6lC 1yh2C 1yrvC 1zdnC 2a4dC 2a7lC 2awfC 2f4wC 2ob4C 2qgxC 2z5dC 3bzhC 3cegC C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 20801.582 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, RESIDUES 201-363 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LOC92912 / Plasmid: PET28-LIC / Production host: Escherichia coli (E. coli) / References: UniProt: Q8WVN8, ubiquitin-protein ligase #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: 2.84 Å3/Da / Density % sol: 56.29 % |
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Crystal grow | Temperature: 298 K / pH: 5.8 Details: NACL, SODIUM CACODYLATE, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K, pH 5.8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9124 |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: May 9, 2005 / Details: MIRRORS |
Radiation | Monochromator: HORIZONTAL BENT SI(111), ASYMMETRICALLY CUT WITH WATER COOLED CU BLOCK Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9124 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→27.07 Å / Num. obs: 36041 / % possible obs: 91.4 % / Observed criterion σ(I): -3 / Redundancy: 2.8 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 22.5 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 2.4 / % possible all: 94.2 |
-Processing
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Refinement | Method to determine structure: SAD / Resolution: 1.8→27.08 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.631 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.126 / ESU R Free: 0.122 / 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: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.471 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→27.08 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.801→1.848 Å / Total num. of bins used: 20
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