+Open data
-Basic information
Entry | Database: PDB / ID: 7wul | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of UBR bof from PRT6 (RDG pH5.5) | ||||||
Components |
| ||||||
Keywords | LIGASE / E3 ligase UBR Box PRT6 | ||||||
Function / homology | Function and homology information ubiquitin-dependent protein catabolic process via the N-end rule pathway / RING-type E3 ubiquitin transferase / ubiquitin protein ligase activity / protein ubiquitination / zinc ion binding Similarity search - Function | ||||||
Biological species | Oryza sativa subsp. japonica (Japanese rice) Oryza sativa (Asian cultivated rice) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å | ||||||
Authors | Ho, M.C. / Cao, C.C. | ||||||
Funding support | Taiwan, 1items
| ||||||
Citation | Journal: To Be Published Title: Crystal structure of UBR box from PRT6 Authors: Ho, M.C. / Cao, J.J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7wul.cif.gz | 31.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7wul.ent.gz | 17.7 KB | Display | PDB format |
PDBx/mmJSON format | 7wul.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7wul_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7wul_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 7wul_validation.xml.gz | 6 KB | Display | |
Data in CIF | 7wul_validation.cif.gz | 7.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wu/7wul ftp://data.pdbj.org/pub/pdb/validation_reports/wu/7wul | HTTPS FTP |
-Related structure data
Related structure data | 7wukC 7wumC 7wunC C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
#1: Protein/peptide | Mass: 347.349 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Oryza sativa (Asian cultivated rice) | ||||
---|---|---|---|---|---|
#2: Protein | Mass: 7919.854 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryza sativa subsp. japonica (Japanese rice) Gene: Os01g0148000, OSNPB_010148000 / Production host: Escherichia coli (E. coli) References: UniProt: A0A0P0UY23, RING-type E3 ubiquitin transferase | ||||
#3: Chemical | #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: 1.78 Å3/Da / Density % sol: 30.94 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 1M sodium citrate, 200mM NaCl, 0.1M Tris |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Jul 25, 2021 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.58→30 Å / Num. obs: 8723 / % possible obs: 99.5 % / Redundancy: 7.6 % / Biso Wilson estimate: 13.12 Å2 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.024 / Rrim(I) all: 0.063 / Χ2: 1.077 / Net I/σ(I): 10.3 / Num. measured all: 65939 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: D_1300027541 Resolution: 1.58→25.18 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.43 / Phase error: 18.87 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 50.51 Å2 / Biso mean: 19.0997 Å2 / Biso min: 8.57 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.58→25.18 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6
|