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- PDB-5bkb: Crystal structure of AAD-1 in complex with (R)-dichlorprop, Mn(II... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5bkb | ||||||
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Title | Crystal structure of AAD-1 in complex with (R)-dichlorprop, Mn(II), and 2-oxoglutarate | ||||||
![]() | (R)-phenoxypropionate/alpha-ketoglutarate-dioxygenase | ||||||
![]() | OXIDOREDUCTASE / dioxygenase / herbicide degradation | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Chekan, J.R. / Nair, S.K. | ||||||
![]() | ![]() 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 | ![]() | 146.7 KB | Display | ![]() |
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PDB format | ![]() | 111.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.1 MB | Display | ![]() |
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Full document | ![]() | 2.1 MB | Display | |
Data in XML | ![]() | 30.1 KB | Display | |
Data in CIF | ![]() | 46.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5bk9C ![]() 5bkcC ![]() 5bkdC ![]() 5bkeC ![]() 1gqwS C: citing same article ( S: Starting model for refinement |
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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
-Protein , 1 types, 2 molecules AB
#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) |
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-Non-polymers , 6 types, 743 molecules ![](data/chem/img/MN.gif)
![](data/chem/img/AKG.gif)
![](data/chem/img/FTV.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/AKG.gif)
![](data/chem/img/FTV.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-FTV / ( | #5: Chemical | #6: Chemical | ChemComp-PEG / | #7: 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: 44.23 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 25% PEG 3350 0.3M LiSO4 0.1M Bicine pH 9.0 8 mg/mL AAD-1 Cryo: 15% glycerol |
-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: Nov 21, 2013 |
Radiation | Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 |
Reflection | Resolution: 1.58→85.9 Å / Num. obs: 80901 / % possible obs: 100 % / Redundancy: 8.1 % / CC1/2: 0.999 / Rsym value: 0.093 / Net I/σ(I): 17.5 |
Reflection shell | Resolution: 1.58→1.587 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.956 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 790 / CC1/2: 0.786 / % possible all: 95.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1GQW Resolution: 1.582→54.196 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.91
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.582→54.196 Å
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Refine LS restraints |
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LS refinement shell |
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