[English] 日本語
Yorodumi- PDB-7nz7: Crystal structure of mouse ADAT2/ADAT3 tRNA deamination complex 1 -
+Open data
-Basic information
Entry | Database: PDB / ID: 7nz7 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of mouse ADAT2/ADAT3 tRNA deamination complex 1 | |||||||||
Components |
| |||||||||
Keywords | HYDROLASE / tRNA modification / wobble adenine / inosine / ADAT / intellectual disability / neurological disorders | |||||||||
Function / homology | Function and homology information tRNA(adenine34) deaminase / tRNA wobble adenosine to inosine editing / tRNA-specific adenosine-34 deaminase activity / tRNA processing / zinc ion binding / nucleus / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.96 Å | |||||||||
Authors | Ramos Morales, E. / Romier, C. | |||||||||
Citation | Journal: Nucleic Acids Res. / Year: 2021 Title: The structure of the mouse ADAT2/ADAT3 complex reveals the molecular basis for mammalian tRNA wobble adenosine-to-inosine deamination. Authors: Ramos-Morales, E. / Bayam, E. / Del-Pozo-Rodriguez, J. / Salinas-Giege, T. / Marek, M. / Tilly, P. / Wolff, P. / Troesch, E. / Ennifar, E. / Drouard, L. / Godin, J.D. / Romier, C. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7nz7.cif.gz | 223.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7nz7.ent.gz | 152.3 KB | Display | PDB format |
PDBx/mmJSON format | 7nz7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7nz7_validation.pdf.gz | 362.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7nz7_full_validation.pdf.gz | 367.7 KB | Display | |
Data in XML | 7nz7_validation.xml.gz | 17.5 KB | Display | |
Data in CIF | 7nz7_validation.cif.gz | 23.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nz/7nz7 ftp://data.pdbj.org/pub/pdb/validation_reports/nz/7nz7 | HTTPS FTP |
-Related structure data
Related structure data | 7nz8C 7nz9C 3dh1S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 21333.463 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Adat2, Deadc1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6P6J0, tRNA(adenine34) deaminase | ||||
---|---|---|---|---|---|
#2: Protein | Mass: 34223.930 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Adat3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6PAT0 | ||||
#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: 5.1 Å3/Da / Density % sol: 75.88 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 7% (W/V) PEG8000, 0.1 M HEPES pH 7.0, 8% ethylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00003 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 22, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00003 Å / Relative weight: 1 |
Reflection | Resolution: 2.96→50 Å / Num. obs: 25887 / % possible obs: 99.9 % / Redundancy: 19.7 % / Biso Wilson estimate: 113.11 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.092 / Net I/σ(I): 26.48 |
Reflection shell | Resolution: 2.96→3.13 Å / Redundancy: 19.7 % / Rmerge(I) obs: 3.82 / Mean I/σ(I) obs: 1.02 / Num. unique obs: 4112 / CC1/2: 0.55 / % possible all: 99.9 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3DH1 Resolution: 2.96→45.94 Å / SU ML: 0.3567 / Cross valid method: FREE R-VALUE / σ(F): 0.45 / Phase error: 31.4172 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: 122.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.96→45.94 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Refine-ID: X-RAY DIFFRACTION
|