[English] 日本語
![](img/lk-miru.gif)
- PDB-6uma: Crystal structure of the TRIM7 B30.2 domain at 1.6 angstrom resolution -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6uma | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the TRIM7 B30.2 domain at 1.6 angstrom resolution | ||||||
![]() | E3 ubiquitin-protein ligase TRIM7 | ||||||
![]() | LIGASE / B30.2 / E3 ubiquitin ligase / PRY/SPRY / TRIM7 | ||||||
Function / homology | ![]() antiviral innate immune response / RING-type E3 ubiquitin transferase / ubiquitin protein ligase activity / protein ubiquitination / Golgi apparatus / zinc ion binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Munoz Sosa, C.J. / Carrizo, M.E. | ||||||
![]() | ![]() Title: Crystal structure and mutational analysis of the human TRIM7 B30.2 domain provide insights into the molecular basis of its binding to glycogenin-1. Authors: Munoz Sosa, C.J. / Issoglio, F.M. / Carrizo, M.E. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 91 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 68.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 467.2 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 470.8 KB | Display | |
Data in XML | ![]() | 17.8 KB | Display | |
Data in CIF | ![]() | 25.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6umbC ![]() 4n7iS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 20274.066 Da / Num. of mol.: 2 / Fragment: B30.2 domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q9C029, RING-type E3 ubiquitin transferase #2: Chemical | ChemComp-MLI / #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.38 % |
---|---|
Crystal grow | Temperature: 283 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: Sodium malonate pH 6.0, glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 16, 2018 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.4586 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.6→20.69 Å / Num. obs: 44099 / % possible obs: 97.6 % / Redundancy: 5.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.042 / Rpim(I) all: 0.019 / Rrim(I) all: 0.046 / Net I/σ(I): 11.3 / Num. measured all: 237684 / Scaling rejects: 95 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 4N7I Resolution: 1.6→20.69 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.963 / SU B: 2.079 / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.092 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 94.48 Å2 / Biso mean: 26.102 Å2 / Biso min: 13.57 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.6→20.69 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.6→1.641 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|