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- PDB-5kag: Crystal structure of a dioxygenase in the Crotonase superfamily in P21 -
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Open data
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Basic information
Entry | Database: PDB / ID: 5kag | ||||||
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Title | Crystal structure of a dioxygenase in the Crotonase superfamily in P21 | ||||||
![]() | (3,5-dihydroxyphenyl)acetyl-CoA 1,2-dioxygenase | ||||||
![]() | OXIDOREDUCTASE / dioxygenase / DpgC | ||||||
Function / homology | ![]() (3,5-dihydroxyphenyl)acetyl-CoA 1,2-dioxygenase / enoyl-CoA hydratase activity / oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen / fatty acid beta-oxidation / antibiotic biosynthetic process / identical protein binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Li, K. / Fielding, E.N. / Condurso, H.L. / Bruner, S.D. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Probing the structural basis of oxygen binding in a cofactor-independent dioxygenase. Authors: Li, K. / Fielding, E.N. / Condurso, H.L. / Bruner, S.D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 975.9 KB | Display | ![]() |
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PDB format | ![]() | 813.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.9 MB | Display | ![]() |
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Full document | ![]() | 2.9 MB | Display | |
Data in XML | ![]() | 177.1 KB | Display | |
Data in CIF | ![]() | 236.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5kahC ![]() 5kajC ![]() 2np9S S: Starting model for refinement 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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Unit cell |
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Components
#1: Protein | ( Mass: 48241.133 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q8KLK7, (3,5-dihydroxyphenyl)acetyl-CoA 1,2-dioxygenase #2: Chemical | ChemComp-YE1 / [( #3: Chemical | ChemComp-OXY / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.31 Å3/Da / Density % sol: 62.87 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 95 mM Na HEPES, 0.94 M NaCl and 1.3 M (NH4)2SO4, pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 13, 2015 |
Radiation | Monochromator: SAGITALLY FOCUSED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.456→43.637 Å / Num. obs: 263454 / % possible obs: 98.5 % / Redundancy: 3.7 % / Biso Wilson estimate: 13.7 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 2.456→2.5 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 2.7 / % possible all: 90.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2NP9 Resolution: 2.456→43.637 Å / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 37.57 / Stereochemistry target values: TWIN_LSQ_F
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.456→43.637 Å
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Refine LS restraints |
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LS refinement shell |
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