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Yorodumi- PDB-6euo: Crystal structure of APO Fe(II)/alpha-ketoglutarate dependent dio... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6euo | ||||||
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Title | Crystal structure of APO Fe(II)/alpha-ketoglutarate dependent dioxygenase KDO5 | ||||||
Components | L-lysine 4-hydroxylase | ||||||
Keywords | OXIDOREDUCTASE / "Fe(II)/alpha-ketoglutarate | ||||||
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 / : / D-MALATE / L-lysine 4-hydroxylase Function and homology information | ||||||
Biological species | Flavobacterium sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Isabet, T. / Stura, E. / Legrand, P. / Zaparucha, A. / Bastard, K. | ||||||
Citation | Journal: Sci Rep / Year: 2018 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6euo.cif.gz | 579.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6euo.ent.gz | 480.9 KB | Display | PDB format |
PDBx/mmJSON format | 6euo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6euo_validation.pdf.gz | 495.7 KB | Display | wwPDB validaton report |
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Full document | 6euo_full_validation.pdf.gz | 513.8 KB | Display | |
Data in XML | 6euo_validation.xml.gz | 55.5 KB | Display | |
Data in CIF | 6euo_validation.cif.gz | 77.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eu/6euo ftp://data.pdbj.org/pub/pdb/validation_reports/eu/6euo | HTTPS FTP |
-Related structure data
Related structure data | 6eurC 6exfC 6exhC 6f2aC 6f2bC 6f2eC 6f6jC 6f9pC C: citing same article (ref.) |
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Similar structure data |
-Links
-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.) Flavobacterium sp. (strain CF136) (bacteria) Gene: PMI10_03368 / Production host: Escherichia coli (E. coli) 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, 543 molecules
#2: Chemical | ChemComp-FE / #3: Chemical | ChemComp-MLT / #4: Chemical | ChemComp-GOL / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.34 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 23% PEG 3350, 200mM Imidazole malate pH7, 150mM Li2SO4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 3, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9801 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→62.2 Å / Num. obs: 67467 / % possible obs: 99.9 % / Redundancy: 9.2 % / Biso Wilson estimate: 56.78 Å2 / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 2.3→2.36 Å / Redundancy: 5 % / Num. unique obs: 4925 / CC1/2: 0.547 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→62.2 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.934 / SU R Cruickshank DPI: 0.291 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.302 / SU Rfree Blow DPI: 0.195 / SU Rfree Cruickshank DPI: 0.196
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Displacement parameters | Biso mean: 70.91 Å2
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Refine analyze | Luzzati coordinate error obs: 0.27 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.3→62.2 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.36 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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