+Open data
-Basic information
Entry | Database: PDB / ID: 1y6l | ||||||
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Title | Human ubiquitin conjugating enzyme E2E2 | ||||||
Components | Ubiquitin-conjugating enzyme E2E2 | ||||||
Keywords | LIGASE / Structural Genomics Consortium / UBIQUITIN / UBIQUITIN-CONJUGATING ENZYME / SGC | ||||||
Function / homology | Function and homology information ISG15 transferase activity / ISG15-protein conjugation / protein K11-linked ubiquitination / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / protein K63-linked ubiquitination / positive regulation of G1/S transition of mitotic cell cycle / protein K48-linked ubiquitination / ubiquitin-protein transferase activity / Antigen processing: Ubiquitination & Proteasome degradation ...ISG15 transferase activity / ISG15-protein conjugation / protein K11-linked ubiquitination / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / protein K63-linked ubiquitination / positive regulation of G1/S transition of mitotic cell cycle / protein K48-linked ubiquitination / ubiquitin-protein transferase activity / Antigen processing: Ubiquitination & Proteasome degradation / DNA damage response / ATP binding / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Walker, J.R. / Avvakumov, G.V. / Newman, E.M. / Mackenzie, F. / Kozieradzki, I. / Bochkarev, A. / Sundstrom, M. / Arrowsmith, C. / Edwards, 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 | 1y6l.cif.gz | 103.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1y6l.ent.gz | 80.5 KB | Display | PDB format |
PDBx/mmJSON format | 1y6l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y6/1y6l ftp://data.pdbj.org/pub/pdb/validation_reports/y6/1y6l | HTTPS FTP |
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-Related structure data
Related structure data | 1yh2C 1yrvC 1zdnC 1zuoC 2a4dC 2a7lC 2awfC 2f4wC 2ob4C 2qgxC 2z5dC 3bzhC 3cegC 1qcqS S: Starting model for refinement C: citing same article (ref.) |
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Similar 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 on special symmetry positions |
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Details | The biological unit is expected to be a monomer. |
-Components
#1: Protein | Mass: 16613.947 Da / Num. of mol.: 3 / Fragment: Residues 55-201 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2E2, UBCH8 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96LR5, ubiquitin-protein ligase #2: 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: 2.34 Å3/Da / Density % sol: 46.95 % |
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Crystal grow | Temperature: 298 K / pH: 8.5 Details: 2M (NH4)2SO4, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 22, 2004 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→19.26 Å / Num. obs: 39009 / % possible obs: 90.5 % / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 23.28 |
Reflection shell | Resolution: 1.85→1.92 Å / % possible all: 91.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1QCQ Resolution: 1.85→20 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.937 / SU B: 3.315 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.158 / ESU R Free: 0.154 / 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: 31.993 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.898 Å / Total num. of bins used: 20
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