[English] 日本語
Yorodumi- PDB-2a7l: Structure of the human hypothetical ubiquitin-conjugating enzyme,... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2a7l | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of the human hypothetical ubiquitin-conjugating enzyme, LOC55284 | ||||||
Components | Hypothetical ubiquitin-conjugating enzyme LOC55284 | ||||||
Keywords | LIGASE / STRUCTURAL GENOMICS CONSORTIUM / (SGC) / UBIQUITIN / UBIQUITIN- CONJUGATING ENZYME | ||||||
Function / homology | Function and homology information N-terminal E2 ubiquitin-conjugating enzyme / protein K11-linked ubiquitination / cellular response to misfolded protein / E2 ubiquitin-conjugating enzyme / protein quality control for misfolded or incompletely synthesized proteins / protein monoubiquitination / ubiquitin conjugating enzyme activity / antiviral innate immune response / negative regulation of TORC1 signaling / Synthesis of active ubiquitin: roles of E1 and E2 enzymes ...N-terminal E2 ubiquitin-conjugating enzyme / protein K11-linked ubiquitination / cellular response to misfolded protein / E2 ubiquitin-conjugating enzyme / protein quality control for misfolded or incompletely synthesized proteins / protein monoubiquitination / ubiquitin conjugating enzyme activity / antiviral innate immune response / negative regulation of TORC1 signaling / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / protein polyubiquitination / ubiquitin-protein transferase activity / Antigen processing: Ubiquitination & Proteasome degradation / proteasome-mediated ubiquitin-dependent protein catabolic process / DNA repair / ubiquitin protein ligase binding / nucleoplasm / ATP binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.82 Å | ||||||
Authors | Walker, J.R. / Avvakumov, G.V. / Xue, S. / Newman, E.M. / Mackenzie, F. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C. / Edwards, A. / Bochkarev, A. ...Walker, J.R. / Avvakumov, G.V. / Xue, S. / Newman, E.M. / 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2a7l.cif.gz | 67 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2a7l.ent.gz | 48.7 KB | Display | PDB format |
PDBx/mmJSON format | 2a7l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2a7l_validation.pdf.gz | 443.5 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2a7l_full_validation.pdf.gz | 445.3 KB | Display | |
Data in XML | 2a7l_validation.xml.gz | 13.6 KB | Display | |
Data in CIF | 2a7l_validation.cif.gz | 18.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a7/2a7l ftp://data.pdbj.org/pub/pdb/validation_reports/a7/2a7l | HTTPS FTP |
-Related structure data
Related structure data | 1y6lSC 1yh2C 1yrvC 1zdnC 1zuoC 2a4dC 2awfC 2f4wC 2ob4C 2qgxC 2z5dC 3bzhC 3cegC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
| ||||||||
Details | The biological unit is a monomer. |
-Components
#1: Protein | Mass: 15159.265 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FLJ11011 / Plasmid: PET28-LIC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q96B02, ubiquitin-protein ligase #2: Chemical | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 52.83 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 3 M NaCl, 0.1 M bisTris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 5, 2005 / 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: 1.8→25 Å / Num. all: 27952 / Num. obs: 27952 / % possible obs: 93.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.2 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 36.68 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.475 / Mean I/σ(I) obs: 1.94 / Num. unique all: 1475 / % possible all: 50.4 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1Y6L Resolution: 1.82→24.44 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.95 / SU B: 4.446 / SU ML: 0.131 / Cross valid method: THROUGHOUT / ESU R: 0.17 / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 36.259 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.82→24.44 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.82→1.862 Å / Total num. of bins used: 20
|