+Open data
-Basic information
Entry | Database: PDB / ID: 2awf | ||||||
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Title | Structure of human Ubiquitin-conjugating enzyme E2 G1 | ||||||
Components | Ubiquitin-conjugating enzyme E2 G1 | ||||||
Keywords | LIGASE / Ubl conjugation pathway / ubiquitin-conjugating enzyme / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / protein K63-linked ubiquitination / 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 / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process ...E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / protein K63-linked ubiquitination / 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 / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / ubiquitin protein ligase binding / extracellular exosome / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Walker, J.R. / Avvakumov, G.V. / Xue, S. / Newman, E.M. / Finerty, P. / Mackenzie, F. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C. / Edwards, A. ...Walker, J.R. / Avvakumov, G.V. / Xue, S. / Newman, E.M. / Finerty, P. / Mackenzie, F. / Weigelt, J. / 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 | 2awf.cif.gz | 39.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2awf.ent.gz | 26.4 KB | Display | PDB format |
PDBx/mmJSON format | 2awf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2awf_validation.pdf.gz | 426.3 KB | Display | wwPDB validaton report |
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Full document | 2awf_full_validation.pdf.gz | 428.2 KB | Display | |
Data in XML | 2awf_validation.xml.gz | 7.3 KB | Display | |
Data in CIF | 2awf_validation.cif.gz | 9.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aw/2awf ftp://data.pdbj.org/pub/pdb/validation_reports/aw/2awf | HTTPS FTP |
-Related structure data
Related structure data | 1y6lC 1yh2C 1yrvC 1zdnC 1zuoC 2a4dC 2a7lC 2f4wC 2ob4C 2qgxC 2z5dC 3bzhC 3cegC 1pzvS 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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Unit cell |
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-Components
#1: Protein | Mass: 19629.270 Da / Num. of mol.: 1 / Fragment: catalytic (UBCc) domain, residues 7-159 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2G1, UBE2G / Plasmid: PET28-LIC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P62253, ubiquitin-protein ligase |
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#2: 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: 3.48 Å3/Da / Density % sol: 64.37 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 24% PEG3350, 0.2 M MgAc, 0.1 M Tris, pH 7.5, 5% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.97985 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 23, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97985 Å / Relative weight: 1 |
Reflection | Resolution: 2.01→39.7 Å / Num. all: 13412 / Num. obs: 13412 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 15.5 % / Rmerge(I) obs: 0.037 / Net I/σ(I): 72.07 |
Reflection shell | Resolution: 2.01→2.08 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.647 / Mean I/σ(I) obs: 2.25 / Num. unique all: 1123 / % possible all: 84.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1PZV Resolution: 2.1→36.98 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.93 / SU B: 5.166 / SU ML: 0.136 / Cross valid method: THROUGHOUT / ESU R: 0.18 / ESU R Free: 0.171 / 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: 49.808 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→36.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.154 Å / Total num. of bins used: 20
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