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- PDB-8b25: Dihydroprecondylocarpine acetate synthase 2 from Tabernanthe ibog... -

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Basic information

Entry
Database: PDB / ID: 8b25
TitleDihydroprecondylocarpine acetate synthase 2 from Tabernanthe iboga - stemmadenine acetate bound structure
ComponentsDihydroprecondylocarpine acetate synthase 2
KeywordsCYTOSOLIC PROTEIN / Alcohol dehydrogenase
Function / homology
Function and homology information


alkaloid metabolic process / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / metal ion binding
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
stemmadenine acetate / Dihydroprecondylocarpine acetate synthase 2
Similarity search - Component
Biological speciesTabernanthe iboga (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 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 1.0Oct 19, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 30, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Jan 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

Downloads & links

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Assembly

Deposited unit
A: Dihydroprecondylocarpine acetate synthase 2
B: Dihydroprecondylocarpine acetate synthase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,98813
Polymers78,5602
Non-polymers1,42811
Water3,027168
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3850 Å2
ΔGint-35 kcal/mol
Surface area25670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.186, 79.845, 130.922
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 5 through 63 or (resid 64...
d_2ens_1(chain "B" and (resid 5 through 6 or (resid 7...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1SERPROA1 - 358
d_12ens_1EDOEDOD
d_21ens_1SERPROH1 - 358
d_22ens_1EDOEDOJ

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), (-0.00159359684052, 0.997046100764, 0.0767888885249), (0.00650507107496, 0.0767976971745, -0.99702547498)
Vector: 110.048619869, -7.33477858761, 188.662592158)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Dihydroprecondylocarpine acetate synthase 2


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 ChemComp-OSO / stemmadenine acetate / methyl (1~{S},2~{S},14~{S})-2-(acetyloxymethyl)-16-ethylidene-4-aza-14-azoniatetracyclo[12.2.2.0^{3,11}.0^{5,10}]octadeca-3(11),5,7,9-tetraene-2-carboxylate


Mass: 397.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H29N2O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.43 Å3/Da / Density % sol: 49.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 23% w/v PEG 3350, 250 mM sodium sulfate and 0.75 mM stemmadenine acetate

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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: Jul 14, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 2.24→2.32 Å / Num. unique obs: 2561 / CC1/2: 0.586

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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: 2.24→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
RfactorNum. reflection% reflection
Rfree0.2206 3385 5.02 %
Rwork0.1739 64083 -
obs0.1761 35719 94.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.78 Å2
Refinement stepCycle: LAST / Resolution: 2.24→39.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5272 0 90 168 5530
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01495469
X-RAY DIFFRACTIONf_angle_d1.46757453
X-RAY DIFFRACTIONf_chiral_restr0.0753876
X-RAY DIFFRACTIONf_plane_restr0.0128954
X-RAY DIFFRACTIONf_dihedral_angle_d7.0469770
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.45339167735 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.24-2.270.4395940.36181742X-RAY DIFFRACTION61.4
2.27-2.30.3751010.32442003X-RAY DIFFRACTION69.9
2.3-2.340.31491130.28312113X-RAY DIFFRACTION74.57
2.34-2.380.30331170.2772257X-RAY DIFFRACTION81.38
2.38-2.420.34211320.2582524X-RAY DIFFRACTION88.09
2.42-2.460.31561450.2392724X-RAY DIFFRACTION96.5
2.46-2.510.2661480.22362769X-RAY DIFFRACTION98.38
2.51-2.560.29161470.21322773X-RAY DIFFRACTION99.56
2.56-2.620.28321500.20912864X-RAY DIFFRACTION99.83
2.62-2.680.2791470.21042801X-RAY DIFFRACTION99.83
2.68-2.750.28291510.21242817X-RAY DIFFRACTION99.93
2.75-2.820.29521530.2142836X-RAY DIFFRACTION99.87
2.82-2.90.2291480.20682794X-RAY DIFFRACTION99.8
2.9-30.26231530.19032820X-RAY DIFFRACTION99.87
3-3.10.21811510.18962826X-RAY DIFFRACTION99.93
3.1-3.230.27651490.1932828X-RAY DIFFRACTION99.97
3.23-3.370.23951510.17982837X-RAY DIFFRACTION99.9
3.38-3.550.26161470.16662805X-RAY DIFFRACTION99.8
3.55-3.780.16321520.15272853X-RAY DIFFRACTION99.9
3.78-4.070.18011470.14592813X-RAY DIFFRACTION99.97
4.07-4.480.16161460.13262816X-RAY DIFFRACTION100
4.48-5.120.16391510.12972817X-RAY DIFFRACTION99.9
5.12-6.450.2171490.15662837X-RAY DIFFRACTION100
6.45-39.920.16841430.15272814X-RAY DIFFRACTION99.56

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