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Yorodumi- PDB-8b25: Dihydroprecondylocarpine acetate synthase 2 from Tabernanthe ibog... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8b25 | |||||||||
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Title | Dihydroprecondylocarpine acetate synthase 2 from Tabernanthe iboga - stemmadenine acetate bound structure | |||||||||
Components | Dihydroprecondylocarpine acetate synthase 2 | |||||||||
Keywords | CYTOSOLIC PROTEIN / Alcohol dehydrogenase | |||||||||
Function / homology | Function and homology information cinnamyl-alcohol dehydrogenase activity / lignin biosynthetic process / alcohol metabolic process / alcohol dehydrogenase (NADP+) activity / metal ion binding Similarity search - Function | |||||||||
Biological species | Tabernanthe iboga (plant) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 Å | |||||||||
Authors | Langley, C. / Basquin, J. / Caputi, L. / O'Connor, S.E. | |||||||||
Funding support | Germany, European Union, 2items
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Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2022 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8b25.cif.gz | 184.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8b25.ent.gz | 118.2 KB | Display | PDB format |
PDBx/mmJSON format | 8b25.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8b25_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 8b25_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 8b25_validation.xml.gz | 30 KB | Display | |
Data in CIF | 8b25_validation.cif.gz | 41.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b2/8b25 ftp://data.pdbj.org/pub/pdb/validation_reports/b2/8b25 | HTTPS FTP |
-Related structure data
Related structure data | 8a3nC 8b1vC 8b26C 8b27C 5fi3S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-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: |
-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.) Tabernanthe iboga (plant) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A5B8X8Z0 |
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-Non-polymers , 5 types, 179 molecules
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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