+Open data
-Basic information
Entry | Database: PDB / ID: 7yrb | ||||||
---|---|---|---|---|---|---|---|
Title | UBR box of human UBR6 | ||||||
Components | F-box protein 11, isoform CRA_fF-box protein | ||||||
Keywords | LIGASE / E3 ubiquitin-protein ligase / UBR-box domain | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.51 Å | ||||||
Authors | Kim, B. / Song, H.K. | ||||||
Funding support | Korea, Republic Of, 1items
| ||||||
Citation | Journal: To Be Published Title: Crystal structure of UBR box from human UBR6 Authors: Kim, B. / Kim, B.H. / Song, H.K. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7yrb.cif.gz | 51.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7yrb.ent.gz | 29.5 KB | Display | PDB format |
PDBx/mmJSON format | 7yrb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yr/7yrb ftp://data.pdbj.org/pub/pdb/validation_reports/yr/7yrb | HTTPS FTP |
---|
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
---|
-Links
-Assembly
Deposited unit |
| ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 9326.521 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FBXO11, hCG_1987171 / Production host: Escherichia coli (E. coli) / References: UniProt: B3KUR1 | ||||||
---|---|---|---|---|---|---|---|
#2: Chemical | #3: Chemical | ChemComp-SO4 / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.85 Å3/Da / Density % sol: 33.67 % |
---|---|
Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 2.2M Ammonium sulfate, 0.1M HEPES sodium pH 7.5, 1% PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1.00003 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 20, 2022 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00003 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. obs: 11429 / % possible obs: 99.8 % / Redundancy: 12.4 % / Biso Wilson estimate: 30.64 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 55.47 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 11.8 % / Rmerge(I) obs: 0.834 / Num. unique obs: 559 / % possible all: 99.6 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MAD / Resolution: 1.51→29.47 Å / SU ML: 0.0811 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.4984 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.64 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.51→29.47 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|