+Open data
-Basic information
Entry | Database: PDB / ID: 7xv7 | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of ZYG11B bound to ORF10 peptide | ||||||||||||
Components | Protein zyg-11 homolog B | ||||||||||||
Keywords | LIGASE / E3 LIGASE | ||||||||||||
Function / homology | Function and homology information Cul2-RING ubiquitin ligase complex / protein quality control for misfolded or incompletely synthesized proteins / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||||||||
Authors | Dong, C. / Yan, X. / Li, Y. | ||||||||||||
Funding support | China, 3items
| ||||||||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2022 Title: Structural insights into ORF10 recognition by ZYG11B. Authors: Zhang, B. / Li, Y. / Feng, Q. / Song, L. / Dong, C. / Yan, X. | ||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7xv7.cif.gz | 235.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7xv7.ent.gz | 171.9 KB | Display | PDB format |
PDBx/mmJSON format | 7xv7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xv/7xv7 ftp://data.pdbj.org/pub/pdb/validation_reports/xv/7xv7 | HTTPS FTP |
---|
-Related structure data
Related structure data | 7ep1S S: Starting model for refinement |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 28541.605 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ZYG11B, KIAA1730 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9C0D3 #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.69 Å3/Da / Density % sol: 54.27 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M MES pH 6.5, 1.6 M MgSO4. |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.987 Å |
Detector | Type: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jul 3, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→37.26 Å / Num. obs: 19576 / % possible obs: 98.11 % / Redundancy: 13.1 % / Biso Wilson estimate: 58.1 Å2 / Rmerge(I) obs: 0.05649 / Net I/σ(I): 31.83 |
Reflection shell | Resolution: 2.6→2.693 Å / Rmerge(I) obs: 0.9676 / Num. unique obs: 1910 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7EP1 Resolution: 2.6→31.21 Å / SU ML: 0.3273 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.6711 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 70.43 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→31.21 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: -37.3578042223 Å / Origin y: -39.3794743586 Å / Origin z: 10.1232240475 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection details: all |