[English] 日本語
![](img/lk-miru.gif)
- PDB-7eus: Crystal structures of 2-oxoglutarate dependent dioxygenase (CTB9)... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 7eus | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structures of 2-oxoglutarate dependent dioxygenase (CTB9) from Cercospora sp. JNU001 | |||||||||||||||
![]() | 2-oxoglutarate (2-OG)-dependent dioxygenase | |||||||||||||||
![]() | OXIDOREDUCTASE / 2-oxoglutarate-dependent dioxygenase / cercosporin | |||||||||||||||
Function / homology | COPPER (II) ION![]() | |||||||||||||||
Biological species | ![]() | |||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||
![]() | Hou, X.D. / Liu, X.Z. / Yuan, Z.B. / Rao, Y.J. | |||||||||||||||
Funding support | ![]()
| |||||||||||||||
![]() | ![]() Title: Molecular Basis of the Unusual Seven-Membered Methylenedioxy Bridge Formation Catalyzed by Fe(II)/alpha-KG-Dependent Oxygenase CTB9 Authors: Liu, X.Z. / Yuan, Z.B. / Su, H. / Hou, X.D. / Deng, Z.W. / Xu, H.B. / Guo, B.D. / Yin, D. / Sheng, X. / Rao, Y.J. | |||||||||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 133 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 107.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 968.9 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 976.5 KB | Display | |
Data in XML | ![]() | 24.5 KB | Display | |
Data in CIF | ![]() | 35 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7eutC ![]() 7euuC C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 39008.090 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-GOL / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.64 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1 mM Bis-Tris pH 6.5, 3% (v/v) glycerol, 25% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 24, 2020 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.29→50 Å / Num. obs: 28264 / % possible obs: 98.6 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.051 / Rrim(I) all: 0.135 / Χ2: 0.878 / Net I/σ(I): 6.1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 80.7 Å2 / Biso mean: 28.651 Å2 / Biso min: 12.93 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.3→42.62 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.291→2.351 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|