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- PDB-7xy9: Cryo-EM structure of secondary alcohol dehydrogenases TbSADH afte... -

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Basic information

Entry
Database: PDB / ID: 7xy9
TitleCryo-EM structure of secondary alcohol dehydrogenases TbSADH after carrier-free immobilization based on weak intermolecular interactions
ComponentsNADP-dependent isopropanol dehydrogenase
KeywordsOXIDOREDUCTASE / Coordination complex / Activity / Stability / Enzyme Immobilization
Function / homology
Function and homology information


isopropanol dehydrogenase (NADP+) / isopropanol dehydrogenase (NADP+) activity / zinc ion binding
Similarity search - Function
Alcohol dehydrogenase, zinc-type, conserved site / Zinc-containing alcohol dehydrogenases signature. / 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
NADP-dependent isopropanol dehydrogenase
Similarity search - Component
Biological speciesThermoanaerobacter brockii (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.12 Å
AuthorsChen, Q. / Li, X. / Yang, F. / Qu, G. / Sun, Z.T. / Wang, Y.J.
Funding support China, 2items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2019YFA0905100 China
National Natural Science Foundation of China (NSFC)21878169 and 21991102 China
CitationJournal: Nat Commun / Year: 2023
Title: Active and stable alcohol dehydrogenase-assembled hydrogels via synergistic bridging of triazoles and metal ions
Authors: Chen, Q. / Qu, G. / Li, X. / Feng, M. / Yang, F. / Li, Y. / Li, J. / Tong, F. / Song, S. / Wang, Y. / Sun, Z. / Luo, G.
History
DepositionJun 1, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 7, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NADP-dependent isopropanol dehydrogenase
B: NADP-dependent isopropanol dehydrogenase
C: NADP-dependent isopropanol dehydrogenase
D: NADP-dependent isopropanol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,55516
Polymers154,0994
Non-polymers45612
Water10,341574
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
NADP-dependent isopropanol dehydrogenase


Mass: 38524.695 Da / Num. of mol.: 4 / Mutation: I86N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoanaerobacter brockii (bacteria) / Gene: adh / Production host: Escherichia coli (E. coli)
References: UniProt: P14941, isopropanol dehydrogenase (NADP+)
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 574 / 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: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: enzyme assembled gel / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Thermoanaerobacter brockii (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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 defocus max: 1600 nm / Nominal defocus min: 700 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: D2 (2x2 fold dihedral)
3D reconstructionResolution: 2.12 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1254312 / Symmetry type: POINT

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