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Open data
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Basic information
Entry | Database: PDB / ID: 5bk9 | |||||||||
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Title | AAD-1 Bound to the Vanadyl Ion and Succinate | |||||||||
![]() | (R)-phenoxypropionate/alpha-ketoglutarate-dioxygenase | |||||||||
![]() | OXIDOREDUCTASE / aryloxyalkanoate dioxygenase / herbicide degradation / BIOSYNTHETIC PROTEIN | |||||||||
Function / homology | ![]() (R)-dichlorprop dioxygenase (2-oxoglutarate) / taurine dioxygenase activity / sulfur compound metabolic process / L-ascorbic acid binding / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Ongpipattanakul, C. / Chekan, J.R. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Molecular basis for enantioselective herbicide degradation imparted by aryloxyalkanoate dioxygenases in transgenic plants. Authors: Chekan, J.R. / Ongpipattanakul, C. / Wright, T.R. / Zhang, B. / Bollinger Jr., J.M. / Rajakovich, L.J. / Krebs, C. / Cicchillo, R.M. / Nair, S.K. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 140.9 KB | Display | ![]() |
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PDB format | ![]() | 107.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 467.9 KB | Display | ![]() |
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Full document | ![]() | 470.7 KB | Display | |
Data in XML | ![]() | 28.3 KB | Display | |
Data in CIF | ![]() | 43.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5bkbC ![]() 5bkcC ![]() 5bkdC ![]() 5bkeC ![]() 1gqwS 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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Unit cell |
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Components
#1: Protein | Mass: 33252.578 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P83310, (R)-dichlorprop dioxygenase (2-oxoglutarate) #2: Chemical | ChemComp-SIN / | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.29 % / Description: Cuboid |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 25% PEG 3350, 0.3 M Li2SO4, and 0.1 M bicine (pH 9.0). Ligands were soaked into crystals. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 28, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9787 Å / Relative weight: 1 |
Reflection | Resolution: 1.51→25 Å / Num. obs: 92316 / % possible obs: 99.2 % / Redundancy: 13.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.07 / Rrim(I) all: 0.076 / Rsym value: 0.072 / Net I/σ(I): 20.5 |
Reflection shell | Resolution: 1.51→1.54 Å / Redundancy: 8.2 % / Num. unique obs: 92316 / Rsym value: 0.792 / % possible all: 99.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1GQW Resolution: 1.51→25 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.472 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.084 / ESU R Free: 0.081 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.397 Å2
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Refinement step | Cycle: 1 / Resolution: 1.51→25 Å
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Refine LS restraints |
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