[English] 日本語
![](img/lk-miru.gif)
- PDB-7ds1: Crystal structure of Aspergillus oryzae Rib2 deaminase in complex... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 7ds1 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Aspergillus oryzae Rib2 deaminase in complex with DARIPP (C-terminal deletion mutant at pH 6.5) | ||||||
![]() | CMP/dCMP-type deaminase domain-containing protein | ||||||
![]() | BIOSYNTHETIC PROTEIN / deaminase / riboflavin | ||||||
Function / homology | Invertebrate-AID/APOBEC-deaminase / diaminohydroxyphosphoribosylaminopyrimidine deaminase activity / Cytidine and deoxycytidylate deaminase domain / Cytidine and deoxycytidylate deaminases domain profile. / Cytidine deaminase-like / nucleobase-containing compound metabolic process / metal ion binding / Chem-HJL / CMP/dCMP-type deaminase domain-containing protein![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Chen, S.C. / Liaw, S.H. / Hsu, C.H. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Crystal structures of Aspergillus oryzae Rib2 deaminase: the functional mechanism involved in riboflavin biosynthesis. Authors: Chen, S.C. / Ye, L.C. / Yen, T.M. / Zhu, R.X. / Li, C.Y. / Chang, S.C. / Liaw, S.H. / Hsu, C.H. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 92.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 68.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 22021.980 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: C-terminal deletion mutant / Source: (gene. exp.) ![]() ![]() ![]() ![]() |
---|---|
#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-HJL / [( |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.72 % |
---|---|
Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop Details: 0.1 M MES pH 6.5, 0.2 M ammonium sulfate and 30% PEG 5000 MME |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Nov 1, 2017 |
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→31.54 Å / Num. obs: 31013 / % possible obs: 100 % / Redundancy: 4.8 % / Biso Wilson estimate: 13.76 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 19.7 |
Reflection shell | Resolution: 1.58→1.64 Å / Rmerge(I) obs: 0.622 / Num. unique obs: 3056 |
-Phasing
Phasing | Method: ![]() |
---|
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]()
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 63.28 Å2 / Biso mean: 20.1704 Å2 / Biso min: 7.55 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.58→31.54 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|