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- EMDB-33514: Cryo-EM structure of secondary alcohol dehydrogenases TbSADH afte... -

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Basic information

Entry
Database: EMDB / ID: EMD-33514
TitleCryo-EM structure of secondary alcohol dehydrogenases TbSADH after carrier-free immobilization based on weak intermolecular interactions
Map data
Sample
  • Complex: enzyme assembled gel
    • Protein or peptide: NADP-dependent isopropanol dehydrogenase
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION
  • Ligand: water
KeywordsCoordination complex / Activity / Stability / Enzyme Immobilization / OXIDOREDUCTASE
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.12 Å
AuthorsChen Q / Li X / Yang F / Qu G / Sun ZT / Wang YJ
Funding support China, 2 items
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, 2022-
Header (metadata) releaseJun 7, 2023-
Map releaseJun 7, 2023-
UpdateDec 20, 2023-
Current statusDec 20, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33514.png

Downloads & links

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Map

FileDownload / File: emd_33514.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.8374 Å
Density
Contour LevelBy AUTHOR: 0.71
Minimum - Maximum-2.0341616 - 3.8801882
Average (Standard dev.)0.0005439131 (±0.10983915)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 251.22 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_33514_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_33514_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : enzyme assembled gel

EntireName: enzyme assembled gel
Components
  • Complex: enzyme assembled gel
    • Protein or peptide: NADP-dependent isopropanol dehydrogenase
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION
  • Ligand: water

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Supramolecule #1: enzyme assembled gel

SupramoleculeName: enzyme assembled gel / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Thermoanaerobacter brockii (bacteria)

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Macromolecule #1: NADP-dependent isopropanol dehydrogenase

MacromoleculeName: NADP-dependent isopropanol dehydrogenase / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: isopropanol dehydrogenase (NADP+)
Source (natural)Organism: Thermoanaerobacter brockii (bacteria)
Molecular weightTheoretical: 38.524695 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MHHHHHHKGF AMLSIGKVGW IEKEKPAPGP FDAIVRPLAV APCTSDIHTV FEGAIGERHN MILGHEAVGE VVEVGSEVKD FKPGDRVVV PANTPDWRTS EVQRGYHQHS GGMLAGWKFS NVKDGVFGEF FHVNDADMNL AHLPKEIPLE AAVMIPDMMT T GFHGAELA ...String:
MHHHHHHKGF AMLSIGKVGW IEKEKPAPGP FDAIVRPLAV APCTSDIHTV FEGAIGERHN MILGHEAVGE VVEVGSEVKD FKPGDRVVV PANTPDWRTS EVQRGYHQHS GGMLAGWKFS NVKDGVFGEF FHVNDADMNL AHLPKEIPLE AAVMIPDMMT T GFHGAELA DIELGATVAV LGIGPVGLMA VAGAKLRGAG RIIAVGSRPV CVDAAKYYGA TDIVNYKDGP IESQIMNLTE GK GVDAAII AGGNADIMAT AVKIVKPGGT IANVNYFGEG EVLPVPRLEW GCGMAHKTIK GGLCPGGRLR MERLIDLVFY KRV DPSKLV THVFRGFDNI EKAFMLMKDK PKDLIKPVVI LA

UniProtKB: NADP-dependent isopropanol dehydrogenase

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Macromolecule #2: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 2 / Number of copies: 4 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 8 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 574 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER / Water

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.7000000000000001 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: D2 (2x2 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 2.12 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1254312
FSC plot (resolution estimation)

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