[English] 日本語
![](img/lk-miru.gif)
- PDB-6f2e: Crystal structure of the APO Fe(II)/alpha-ketoglutarate dependent... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6f2e | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the APO Fe(II)/alpha-ketoglutarate dependent dioxygenase KDO1 | ||||||
![]() | L-lysine 3-hydroxylase | ||||||
![]() | OXIDOREDUCTASE / Fe(II)/alpha-ketoglutarate / dioxygenases / enzyme / FeII alphaKG form / oxydoreductase | ||||||
Function / homology | Clavaminate synthase-like / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor / Taurine catabolism dioxygenase TauD, TfdA family / Taurine dioxygenase TauD-like superfamily / 2-oxoglutarate-dependent dioxygenase activity / iron ion binding / ACETIC ACID / L-lysine 3-hydroxylase![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Isabet, T. / Stura, E.A. / Legrand, P. / Zaparucha, A. / Bastard, K. | ||||||
![]() | ![]() Title: Structural Studies based on two Lysine Dioxygenases with Distinct Regioselectivity Brings Insights Into Enzyme Specificity within the Clavaminate Synthase-Like Family. Authors: Bastard, K. / Isabet, T. / Stura, E.A. / Legrand, P. / Zaparucha, A. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 544.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 450.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 468 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 481.3 KB | Display | |
Data in XML | ![]() | 60.7 KB | Display | |
Data in CIF | ![]() | 91.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6euoC ![]() 6eurC ![]() 6exfC ![]() 6exhC ![]() 6f2aC ![]() 6f2bC ![]() 6f6jC ![]() 6f9pC C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
3 | ![]()
| ||||||||
4 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 39236.211 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: Caci_0231 / Production host: ![]() ![]() References: UniProt: C7QJ42, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor #2: Chemical | ChemComp-ACY / #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.63 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: KDO1 : 9.3 mg/ml in 0.2 M NaCl, .001 M DTT, 0.05M Tris-HCl, pH 8 Precipitant : 18% PEG3350, 0.15 M Tris pH 7.5, 0.3 M Na Acetate Soaking/cryo : 20% PEG3350, 0.15 M Tris pH 7.5, 0.3 M Na Acetate, 20% glycerol PH range: 7.5-8.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 13, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 117676 / % possible obs: 98.5 % / Redundancy: 4.65 % / Biso Wilson estimate: 29.66 Å2 / CC1/2: 0.997 / Rrim(I) all: 0.0117 / Net I/σ(I): 10.24 |
Reflection shell | Resolution: 1.9→1.95 Å / Redundancy: 3.45 % / Mean I/σ(I) obs: 1.31 / Num. unique obs: 29174 / CC1/2: 0.668 / % possible all: 95.6 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]()
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.56 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.22 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.9→38 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.9→1.95 Å / Total num. of bins used: 20
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|