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- PDB-8b27: Dihydroprecondylocarpine acetate synthase from Catharanthus roseus -

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Basic information

Entry
Database: PDB / ID: 8b27
TitleDihydroprecondylocarpine acetate synthase from Catharanthus roseus
ComponentsDehydroprecondylocarpine acetate synthase
KeywordsCYTOSOLIC PROTEIN / Alcohol dehydrogenase
Function / homology
Function and homology information


cinnamyl-alcohol dehydrogenase activity / lignin biosynthetic process / alkaloid biosynthetic process / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / protein homodimerization activity / metal ion binding / cytosol
Similarity search - Function
: / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase / GroES-like superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Dehydroprecondylocarpine acetate synthase
Similarity search - Component
Biological speciesCatharanthus roseus (Madagascar periwinkle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsLangley, C. / Basquin, J. / Caputi, L. / O'Connor, S.E.
Funding support Germany, European Union, 2items
OrganizationGrant numberCountry
Max Planck Society Germany
European Research Council (ERC)788301European Union
CitationJournal: 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
DepositionSep 13, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 2, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dehydroprecondylocarpine acetate synthase
B: Dehydroprecondylocarpine acetate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,4587
Polymers77,9772
Non-polymers4805
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2270 Å2
ΔGint-69 kcal/mol
Surface area25500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.019, 114.015, 143.357
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 12 through 183 or (resid 184...
d_2ens_1(chain "B" and ((resid 12 through 14 and (name N...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ILESERA1 - 318
d_21ens_1ILETYRB3 - 92
d_22ens_1CYSSERB94 - 321

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), (-0.0231863526086, -0.999521579826, 0.0204695997966), (-0.973276992571, 0.0272470943566, 0.228012042623)
Vector: -35.2548254593, 39.6870011313, -28.3522095735)

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Components

#1: Protein Dehydroprecondylocarpine acetate synthase


Mass: 38988.711 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Catharanthus roseus (Madagascar periwinkle)
Gene: DPAS, Caros004542, Cr033537 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A1B1FHP3, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.2 Å3/Da / Density % sol: 61.53 %
Crystal growTemperature: 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+

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 2.45→2.538 Å / Num. unique obs: 3719 / CC1/2: 0.879

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Processing

Software
NameVersionClassification
PHENIX1.19rc6_4061refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5fi3

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
RfactorNum. reflection% reflection
Rfree0.2552 3579 5.02 %
Rwork0.2306 67709 -
obs0.2318 37564 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 62.75 Å2
Refinement stepCycle: LAST / Resolution: 2.45→46.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4566 0 25 60 4651
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00394660
X-RAY DIFFRACTIONf_angle_d0.7486350
X-RAY DIFFRACTIONf_chiral_restr0.052770
X-RAY DIFFRACTIONf_plane_restr0.0052820
X-RAY DIFFRACTIONf_dihedral_angle_d5.4893669
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.878796981836 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.480.28151330.31562517X-RAY DIFFRACTION97.43
2.48-2.510.32341350.27672599X-RAY DIFFRACTION100
2.51-2.550.32751370.28062608X-RAY DIFFRACTION100
2.55-2.590.28341380.26462598X-RAY DIFFRACTION100
2.59-2.630.27481370.26232583X-RAY DIFFRACTION99.96
2.63-2.670.28491400.27122620X-RAY DIFFRACTION99.93
2.67-2.710.33751380.2942615X-RAY DIFFRACTION100
2.71-2.760.34321460.30252628X-RAY DIFFRACTION100
2.76-2.820.26011380.27032591X-RAY DIFFRACTION100
2.82-2.870.36251410.26762613X-RAY DIFFRACTION100
2.87-2.940.27831290.26122641X-RAY DIFFRACTION99.93
2.94-3.010.30191300.24722561X-RAY DIFFRACTION99.93
3.01-3.080.30421400.26022643X-RAY DIFFRACTION100
3.08-3.160.27911370.26632585X-RAY DIFFRACTION100
3.16-3.260.27751350.26772618X-RAY DIFFRACTION99.93
3.26-3.360.32311370.26192622X-RAY DIFFRACTION100
3.36-3.480.28571390.23242581X-RAY DIFFRACTION100
3.48-3.620.2181350.22782625X-RAY DIFFRACTION100
3.62-3.790.261420.22072645X-RAY DIFFRACTION100
3.79-3.990.21031370.21982569X-RAY DIFFRACTION100
3.99-4.240.23471370.20912597X-RAY DIFFRACTION100
4.24-4.560.20761400.18482605X-RAY DIFFRACTION100
4.56-5.020.2841330.19012632X-RAY DIFFRACTION100
5.02-5.750.2551440.23272603X-RAY DIFFRACTION100
5.75-7.230.25751390.2382604X-RAY DIFFRACTION100
7.24-46.460.17991420.19572606X-RAY DIFFRACTION100

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