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- PDB-7o6p: Structure of the borneol dehydrogenase 2 of Salvia officinalis -

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Entry
Database: PDB / ID: 7o6p
TitleStructure of the borneol dehydrogenase 2 of Salvia officinalis
Componentsborneol dehydrogenase
KeywordsOXIDOREDUCTASE / TERPENOID / ALCOHOL / BORNEOL / ROSSMANN-LIKE FOLD
Biological speciesSalvia officinalis (garden sage)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.04 Å
AuthorsDimos, N. / Helmer, C.P.O. / Hilal, T. / Loll, B.
Funding support Germany, Austria, 6items
OrganizationGrant numberCountry
German Federal Ministry for Education and Research031B050B Germany
Austrian Science FundP31001-B29 Austria
German Research Foundation (DFG)INST 335/588-1 Germany
German Research Foundation (DFG)INST 335/589-1 Germany
German Research Foundation (DFG)INST 335/590-1 Germany
German Research Foundation (DFG)HA 2549/15-2 Germany
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2022
Title: CryoEM analysis of small plant biocatalysts at sub-2 Å resolution.
Authors: Nicole Dimos / Carl P O Helmer / Andrea M Chánique / Markus C Wahl / Robert Kourist / Tarek Hilal / Bernhard Loll /
Abstract: Enzyme catalysis has emerged as a key technology for developing efficient, sustainable processes in the chemical, biotechnological and pharmaceutical industries. Plants provide large and diverse ...Enzyme catalysis has emerged as a key technology for developing efficient, sustainable processes in the chemical, biotechnological and pharmaceutical industries. Plants provide large and diverse pools of biosynthetic enzymes that facilitate complex reactions, such as the formation of intricate terpene carbon skeletons, with exquisite specificity. High-resolution structural analysis of these enzymes is crucial in order to understand their mechanisms and modulate their properties by targeted engineering. Although cryo-electron microscopy (cryoEM) has revolutionized structural biology, its applicability to high-resolution structural analysis of comparatively small enzymes has so far been largely unexplored. Here, it is shown that cryoEM can reveal the structures of plant borneol dehydrogenases of ∼120 kDa at or below 2 Å resolution, paving the way for the rapid development of new biocatalysts that can provide access to bioactive terpenes and terpenoids.
History
DepositionApr 12, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 1, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 19, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

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Assembly

Deposited unit
A: borneol dehydrogenase
B: borneol dehydrogenase
C: borneol dehydrogenase
D: borneol dehydrogenase


Theoretical massNumber of molelcules
Total (without water)129,0704
Polymers129,0704
Non-polymers00
Water4,828268
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area18070 Å2
ΔGint-118 kcal/mol
Surface area34310 Å2

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Components

#1: Protein
borneol dehydrogenase


Mass: 32267.602 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salvia officinalis (garden sage) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 268 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Homotetrameric complex of borneol dehydrogenase / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: YES
Source (natural)Organism: Salvia officinalis (garden sage)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.5
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid type: UltrAuFoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 96000 X / Nominal defocus max: 1600 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 40 sec. / Electron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 1439

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Processing

SoftwareName: PHENIX / Version: 1.19.1_4122: / Classification: refinement
EM software
IDNameVersionCategory
1cryoSPARC2.19particle selection
2EPU2.9image acquisition
4cryoSPARC2.19CTF correction
10cryoSPARC2.19initial Euler assignment
11cryoSPARC2.19final Euler assignment
12cryoSPARCclassification
13cryoSPARC2.193D reconstruction
14ARP/wARP3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 155724
SymmetryPoint symmetry: D2 (2x2 fold dihedral)
3D reconstructionResolution: 2.04 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 173781 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0088168
ELECTRON MICROSCOPYf_angle_d0.58211080
ELECTRON MICROSCOPYf_dihedral_angle_d11.7333002
ELECTRON MICROSCOPYf_chiral_restr0.0491264
ELECTRON MICROSCOPYf_plane_restr0.0051468

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