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- PDB-8b26: Dihydroprecondylocarpine acetate synthase 2 from Tabernanthe iboga -
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Open data
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Basic information
Entry | Database: PDB / ID: 8b26 | |||||||||
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Title | Dihydroprecondylocarpine acetate synthase 2 from Tabernanthe iboga | |||||||||
![]() | 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 | ![]() | 144.7 KB | Display | ![]() |
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PDB format | ![]() | 111.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 434.6 KB | Display | ![]() |
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Full document | ![]() | 438.7 KB | Display | |
Data in XML | ![]() | 25.5 KB | Display | |
Data in CIF | ![]() | 34.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8a3nC ![]() 8b1vC ![]() 8b25C ![]() 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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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: PRO / End label comp-ID: PRO / Auth seq-ID: 5 - 362 / Label seq-ID: 5 - 362
NCS ensembles : (Details: Local NCS retraints between domains: 1 2) NCS oper: (Code: givenMatrix: (-0.99975576381, 0.0217010823587, -0.00418040108903), (0.0213397738527, 0.997122668285, 0.0727392496772), (0.00574689313635, 0.0726322753062, -0.997342231034)Vector: 110. ...NCS oper: (Code: given Matrix: (-0.99975576381, 0.0217010823587, -0.00418040108903), Vector: |
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Components
#1: Protein | Mass: 39280.113 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.33 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 17% w/v PEG 3350, 200 mM ammonium chloride and 0.75 mM angryline |
-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: 2.42→41.64 Å / Num. obs: 29565 / % possible obs: 98.98 % / Redundancy: 11.6 % / Biso Wilson estimate: 64.9 Å2 / CC1/2: 0.99 / Net I/σ(I): 16.49 |
Reflection shell | Resolution: 2.42→2.5 Å / Num. unique obs: 2702 / CC1/2: 0.785 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5FI3 Resolution: 2.42→41.64 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.06 / Stereochemistry target values: ML
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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: 2.42→41.64 Å
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Refine LS restraints |
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LS refinement shell |
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