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- PDB-5bkc: Crystal structure of AAD-1 in complex with (R)-diclofop, Mn(II), ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5bkc | ||||||
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Title | Crystal structure of AAD-1 in complex with (R)-diclofop, Mn(II), and 2-oxoglutarate | ||||||
![]() | (R)-phenoxypropionate/alpha-ketoglutarate-dioxygenase | ||||||
![]() | ![]() ![]() | ||||||
Function / homology | ![]() (R)-dichlorprop dioxygenase (2-oxoglutarate) / ![]() ![]() ![]() ![]() 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 | ![]() | 144 KB | Display | ![]() |
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PDB format | ![]() | 109.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5bk9C ![]() 5bkbC ![]() 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 , 5 types, 675 molecules ![](data/chem/img/MN.gif)
![](data/chem/img/AKG.gif)
![](data/chem/img/O0D.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/AKG.gif)
![](data/chem/img/O0D.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ![]() #4: Chemical | ChemComp-O0D / ( | #5: Chemical | ![]() #6: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.14 % |
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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 225 mm CCD / Detector: CCD / Date: Feb 23, 2014 |
Radiation | Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.8→85.8 Å / Num. obs: 55192 / % possible obs: 100 % / Redundancy: 9.2 % / CC1/2: 0.999 / Rsym value: 0.111 / Net I/av σ(I): 0.999 / Net I/σ(I): 18.7 |
Reflection shell | Resolution: 1.8→1.806 Å / Mean I/σ(I) obs: 2.6 / Num. unique obs: 541 / CC1/2: 0.801 / Rsym value: 0.929 / % possible all: 97.3 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 1GQW Resolution: 1.8→48.85 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.09
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→48.85 Å
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Refine LS restraints |
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LS refinement shell |
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