+Open data
-Basic information
Entry | Database: PDB / ID: 7o6q | |||||||||||||||||||||
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Title | Structure of the borneol dehydrogenase 1 of salvia rosmarinus | |||||||||||||||||||||
Components | borneol dehydrogenase | |||||||||||||||||||||
Keywords | OXIDOREDUCTASE / TERPENOID / ALCOHOL / BORNEOL / ROSSMANN-LIKE FOLD | |||||||||||||||||||||
Biological species | Salvia rosmarinus (rosemary) | |||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 1.88 Å | |||||||||||||||||||||
Authors | Dimos, N. / Helmer, C.P.O. / Hilal, T. / Loll, B. | |||||||||||||||||||||
Funding support | Germany, Austria, 6items
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Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7o6q.cif.gz | 179.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7o6q.ent.gz | 143.4 KB | Display | PDB format |
PDBx/mmJSON format | 7o6q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7o6q_validation.pdf.gz | 801.8 KB | Display | wwPDB validaton report |
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Full document | 7o6q_full_validation.pdf.gz | 807.6 KB | Display | |
Data in XML | 7o6q_validation.xml.gz | 37.4 KB | Display | |
Data in CIF | 7o6q_validation.cif.gz | 58.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o6/7o6q ftp://data.pdbj.org/pub/pdb/validation_reports/o6/7o6q | HTTPS FTP |
-Related structure data
Related structure data | 12740MC 7o6pC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 30284.529 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salvia rosmarinus (rosemary) / Production host: Escherichia coli BL21(DE3) (bacteria) #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Homotetrameric complex of borneol dehydrogenase / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Molecular weight | Experimental value: YES |
Source (natural) | Organism: Salvia rosmarinus (rosemary) |
Source (recombinant) | Organism: Escherichia coli BL21(DE3) (bacteria) |
Buffer solution | pH: 7.5 |
Specimen | Conc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid type: UltrAuFoil R1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 120000 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 holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 30 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: 1666 |
-Processing
Software | Name: PHENIX / Version: 1.19.1_4122: / Classification: refinement | ||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 1635690 | ||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: D2 (2x2 fold dihedral) | ||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 1.88 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 210505 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||
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