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- PDB-8b27: Dihydroprecondylocarpine acetate synthase from Catharanthus roseus -
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Open data
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Basic information
Entry | Database: PDB / ID: 8b27 | |||||||||
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Title | Dihydroprecondylocarpine acetate synthase from Catharanthus roseus | |||||||||
![]() | Dehydroprecondylocarpine acetate synthase | |||||||||
![]() | CYTOSOLIC PROTEIN / Alcohol dehydrogenase | |||||||||
Function / homology | ![]() alkaloid biosynthetic process / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / oxidoreductase activity / protein homodimerization activity / metal ion binding / cytosol 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 | ![]() | 158.9 KB | Display | ![]() |
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PDB format | ![]() | 99.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 451.6 KB | Display | ![]() |
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Full document | ![]() | 464 KB | Display | |
Data in XML | ![]() | 24.5 KB | Display | |
Data in CIF | ![]() | 33.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8a3nC ![]() 8b1vC ![]() 8b25C ![]() 8b26C ![]() 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: (-0.228460694179, -0.0146358229099, -0.97344311796), (-0.0231863526086, -0.999521579826, 0.0204695997966), (-0.973276992571, 0.0272470943566, 0.228012042623)Vector: -35. ...NCS oper: (Code: given Matrix: (-0.228460694179, -0.0146358229099, -0.97344311796), Vector: |
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Components
#1: Protein | Mass: 38988.711 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: DPAS, Caros004542, Cr033537 / Production host: ![]() ![]() References: UniProt: A0A1B1FHP3, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor #2: Chemical | ChemComp-SO4 / #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: 3.2 Å3/Da / Density % sol: 61.53 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 1.26 M ammonium sulfate, 100 mM TRIS buffer pH 8.5 and 200mM lithium sulfate 1 mM NADP+ |
-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: Nov 19, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→46.46 Å / Num. obs: 37564 / % possible obs: 99.96 % / Redundancy: 13.2 % / Biso Wilson estimate: 53.35 Å2 / CC1/2: 0.99 / Net I/σ(I): 21.46 |
Reflection shell | Resolution: 2.45→2.538 Å / Num. unique obs: 3719 / CC1/2: 0.879 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5fi3 Resolution: 2.45→46.46 Å / SU ML: 0.318 / Cross valid method: FREE R-VALUE / σ(F): 1.28 / Phase error: 26.2192 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: 62.75 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.45→46.46 Å
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Refine LS restraints |
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Refine LS restraints NCS | Type: Torsion NCS / Rms dev position: 0.878796981836 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
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