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- PDB-8b26: Dihydroprecondylocarpine acetate synthase 2 from Tabernanthe iboga -

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Basic information

Entry
Database: PDB / ID: 8b26
TitleDihydroprecondylocarpine acetate synthase 2 from Tabernanthe iboga
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
Dihydroprecondylocarpine acetate synthase 2
Similarity search - Component
Biological speciesTabernanthe iboga (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42 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 ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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)78,6914
Polymers78,5602
Non-polymers1312
Water54030
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2220 Å2
ΔGint-17 kcal/mol
Surface area27380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.422, 78.124, 131.207
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
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_1A
d_2ens_1B

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

Dom-IDAuth asym-IDLabel asym-ID
d_1AA
d_2B - AB - A

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), (0.0213397738527, 0.997122668285, 0.0727392496772), (0.00574689313635, 0.0726322753062, -0.997342231034)
Vector: 110.703806914, -8.66450259731, 189.607690417)

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Components

#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
#2: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 30 / 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: 2.43 Å3/Da / Density % sol: 49.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 17% w/v PEG 3350, 200 mM ammonium chloride and 0.75 mM angryline

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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: 2.42→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 shellResolution: 2.42→2.5 Å / Num. unique obs: 2702 / CC1/2: 0.785

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5FI3

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
RfactorNum. reflection% reflection
Rfree0.2575 2786 5.01 %
Rwork0.2139 --
obs0.216 29565 98.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.42→41.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5278 0 2 30 5310
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035378
X-RAY DIFFRACTIONf_angle_d0.6937332
X-RAY DIFFRACTIONf_dihedral_angle_d5.471760
X-RAY DIFFRACTIONf_chiral_restr0.048873
X-RAY DIFFRACTIONf_plane_restr0.005946
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.42-2.460.47061270.39732357X-RAY DIFFRACTION89
2.46-2.510.39211350.36922522X-RAY DIFFRACTION94
2.51-2.560.38211360.34152605X-RAY DIFFRACTION98
2.56-2.610.39021410.32992661X-RAY DIFFRACTION100
2.61-2.660.39361360.30842658X-RAY DIFFRACTION100
2.66-2.730.43261400.29282645X-RAY DIFFRACTION100
2.73-2.790.32431430.28792688X-RAY DIFFRACTION100
2.8-2.870.29681420.27972666X-RAY DIFFRACTION100
2.87-2.960.38021390.25412660X-RAY DIFFRACTION100
2.96-3.050.26461440.2672675X-RAY DIFFRACTION100
3.05-3.160.22521400.25392658X-RAY DIFFRACTION100
3.16-3.290.30631350.26542685X-RAY DIFFRACTION100
3.29-3.440.32221370.23772651X-RAY DIFFRACTION100
3.44-3.620.24691370.23682712X-RAY DIFFRACTION100
3.62-3.840.24791440.21242645X-RAY DIFFRACTION100
3.84-4.140.25671470.1982697X-RAY DIFFRACTION100
4.14-4.560.20531440.17722646X-RAY DIFFRACTION100
4.56-5.210.15961420.16472681X-RAY DIFFRACTION100
5.21-6.560.28781400.19382664X-RAY DIFFRACTION100
6.57-41.640.21481370.16062674X-RAY DIFFRACTION100

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