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- PDB-8b25: Dihydroprecondylocarpine acetate synthase 2 from Tabernanthe ibog... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8b25 | |||||||||
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Title | Dihydroprecondylocarpine acetate synthase 2 from Tabernanthe iboga - stemmadenine acetate bound structure | |||||||||
![]() | Dihydroprecondylocarpine acetate synthase 2 | |||||||||
![]() | CYTOSOLIC PROTEIN / Alcohol dehydrogenase | |||||||||
Function / homology | ![]() cinnamyl-alcohol dehydrogenase activity / lignin biosynthetic process / alcohol metabolic process / alcohol dehydrogenase (NADP+) activity / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Langley, C. / Basquin, J. / Caputi, L. / O'Connor, S.E. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Expansion of the Catalytic Repertoire of Alcohol Dehydrogenases in Plant Metabolism. Authors: Langley, C. / Tatsis, E. / Hong, B. / Nakamura, Y. / Paetz, C. / Stevenson, C.E.M. / Basquin, J. / Lawson, D.M. / Caputi, L. / O'Connor, S.E. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 184.9 KB | Display | ![]() |
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PDB format | ![]() | 118.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 30 KB | Display | |
Data in CIF | ![]() | 41.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8a3nC ![]() 8b1vC ![]() 8b26C ![]() 8b27C ![]() 5fi3S S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper: (Code: givenMatrix: (-0.999977571998, -0.00108933946923, -0.00660824031806), (-0.00159359684052, 0.997046100764, 0.0767888885249), (0.00650507107496, 0.0767976971745, -0.99702547498)Vector: ...NCS oper: (Code: given Matrix: (-0.999977571998, -0.00108933946923, -0.00660824031806), Vector: |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 39280.113 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 179 molecules ![](data/chem/img/OSO.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-EDO / #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.48 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 23% w/v PEG 3350, 250 mM sodium sulfate and 0.75 mM stemmadenine acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 14, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.24→39.92 Å / Num. obs: 35719 / % possible obs: 94.79 % / Redundancy: 12.1 % / Biso Wilson estimate: 44.54 Å2 / CC1/2: 0.999 / Net I/σ(I): 17.69 |
Reflection shell | Resolution: 2.24→2.32 Å / Num. unique obs: 2561 / CC1/2: 0.586 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5FI3 Resolution: 2.24→39.92 Å / SU ML: 0.327 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 26.0979 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.78 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.24→39.92 Å
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Refine LS restraints |
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Refine LS restraints NCS | Type: Torsion NCS / Rms dev position: 1.45339167735 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
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