+
Open data
-
Basic information
Entry | Database: PDB / ID: 2qgx | ||||||
---|---|---|---|---|---|---|---|
Title | Ubiquitin-conjugating enzyme E2Q | ||||||
![]() | Ubiquitin-conjugating enzyme E2 Q1 | ||||||
![]() | LIGASE / ubiquitin conjugating protein / UBC / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | ![]() prolactin secretion / reproductive system development / fertilization / mating behavior / E2 ubiquitin-conjugating enzyme / suckling behavior / ubiquitin conjugating enzyme activity / embryo implantation / filopodium / protein polyubiquitination ...prolactin secretion / reproductive system development / fertilization / mating behavior / E2 ubiquitin-conjugating enzyme / suckling behavior / ubiquitin conjugating enzyme activity / embryo implantation / filopodium / protein polyubiquitination / Antigen processing: Ubiquitination & Proteasome degradation / ATP binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Neculai, D. / Avvakumov, G.V. / Xue, S. / Walker, J.R. / Mackenzie, F. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. ...Neculai, D. / Avvakumov, G.V. / Xue, S. / Walker, J.R. / Mackenzie, F. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Sicheri, F. / Dhe-Paganon, S. / Structural Genomics Consortium (SGC) | ||||||
![]() | ![]() 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: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 269 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 219.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 391 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 409.5 KB | Display | |
Data in XML | ![]() | 15 KB | Display | |
Data in CIF | ![]() | 22.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1y6lC ![]() 1yh2C ![]() 1yrvC ![]() 1zdnC ![]() 1zuoSC ![]() 2a4dC ![]() 2a7lC ![]() 2awfC ![]() 2f4wC ![]() 2ob4C ![]() 2z5dC ![]() 3bzhC ![]() 3cegC S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
3 | ![]()
| ||||||||
4 | ![]()
| ||||||||
5 | ![]()
| ||||||||
6 | ![]()
| ||||||||
Unit cell |
| ||||||||
Details | biological unit is 1/4 asymmetric unit. |
-
Components
#1: Protein | Mass: 18868.420 Da / Num. of mol.: 4 / Fragment: UBC domain; residues 248-414 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 48.98 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 7.5 Details: 22% PEG4000, 0.1 M Tris-Cl, pH7.5, 0.12 M MgCl2, 1 mM DTT, vapor diffusion, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 14, 2006 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Av σ(I) over netI: 15.81 / Number: 122268 / Rmerge(I) obs: 0.039 / D res high: 2.55 Å / Num. obs: 44274 / % possible obs: 96.7 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.55→38.722 Å / Num. obs: 22493 / % possible obs: 96.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 63.455 Å2 / Rmerge(I) obs: 0.039 / Net I/σ(I): 15.81 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Phasing
Phasing MR |
|
---|
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 1ZUO Resolution: 2.56→38.722 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.807 / Stereochemistry target values: twin_lsq_f
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Bsol: 88.392 Å2 / ksol: 0.394 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 593.55 Å2 / Biso mean: 84.773 Å2 / Biso min: 23.96 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.56→38.722 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|