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- PDB-6exh: Crystal structure of the complex Fe(II)/alpha-ketoglutarate depen... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6exh | ||||||
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Title | Crystal structure of the complex Fe(II)/alpha-ketoglutarate dependent dioxygenase KDO5 with Fe(II)/succinate/(4R)-4-hydroxy-L-lysine | ||||||
![]() | L-lysine 4-hydroxylase | ||||||
![]() | OXIDOREDUCTASE / Fe(II)/alpha-ketoglutarate / dioxygenases / enzyme / FeII alphaKG form / oxydoreductase | ||||||
Function / homology | 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 dioxygenase TauD-like superfamily / 2-oxoglutarate-dependent dioxygenase activity / metal ion binding / : / 4-HYDROXY-LYSINE / SUCCINIC ACID / L-lysine 4-hydroxylase![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Isabet, T. / Stura, E. / 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 580.3 KB | Display | ![]() |
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PDB format | ![]() | 482.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 496.1 KB | Display | ![]() |
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Full document | ![]() | 515.4 KB | Display | |
Data in XML | ![]() | 55.7 KB | Display | |
Data in CIF | ![]() | 76.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6euoC ![]() 6eurC ![]() 6exfC ![]() 6f2aC ![]() 6f2bC ![]() 6f2eC ![]() 6f6jC ![]() 6f9pC C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 41817.129 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: J3BZS6, 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 |
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-Non-polymers , 5 types, 448 molecules ![](data/chem/img/FE.gif)
![](data/chem/img/LYO.gif)
![](data/chem/img/SIN.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/LYO.gif)
![](data/chem/img/SIN.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-FE / #3: Chemical | ChemComp-LYO / #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.4 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 25% PEG4000, 0.2M Imidazole malate pH7, 0.15M Li2SO4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 8, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9801 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→63.57 Å / Num. obs: 47269 / % possible obs: 99.8 % / Redundancy: 13.7 % / CC1/2: 0.999 / Rrim(I) all: 0.165 / Net I/σ(I): 13.86 |
Reflection shell | Resolution: 2.6→2.76 Å / Mean I/σ(I) obs: 1.4 / Num. unique obs: 7484 / CC1/2: 0.84 / Rrim(I) all: 1.56 / % possible all: 99 |
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Processing
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Refinement | Method to determine structure: ![]()
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Displacement parameters | Biso mean: 79.54 Å2
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Refine analyze | Luzzati coordinate error obs: 0.32 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.6→38.07 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.67 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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