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- EMDB-50550: Aldehyde dehydrogenase -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-50550
TitleAldehyde dehydrogenase
Map datarelion blush map
Sample
  • Complex: PDEN_2366
    • Protein or peptide: Aldehyde dehydrogenase
  • Ligand: POTASSIUM ION
KeywordsAldehyde dehydrogenase / tetramer / oxidoreductase
Function / homology
Function and homology information


acetaldehyde dehydrogenase (NAD+) activity / aldehyde dehydrogenase (NAD+)
Similarity search - Function
Aldehyde dehydrogenase, glutamic acid active site / Aldehyde dehydrogenases glutamic acid active site. / Aldehyde dehydrogenase, cysteine active site / Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, C-terminal / Aldehyde dehydrogenase, N-terminal / Aldehyde/histidinol dehydrogenase
Similarity search - Domain/homology
Aldehyde dehydrogenase
Similarity search - Component
Biological speciesParacoccus denitrificans (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsLamers MH / Schada von Borzyskowski L / Ren M
Funding support China, 1 items
OrganizationGrant numberCountry
Chinese Scholarship CouncilCSC202207720003 China
CitationJournal: To Be Published
Title: Aldehyde dehydrogenase
Authors: Lamers MH / Schada von Borzyskowski L / Ren M
History
DepositionJun 5, 2024-
Header (metadata) releaseJun 11, 2025-
Map releaseJun 11, 2025-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50550.png

Downloads & links

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Map

FileDownload / File: emd_50550.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationrelion blush map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 256 pix.
= 214.016 Å		0.84 Å/pix.
x 256 pix.
= 214.016 Å		0.84 Å/pix.
x 256 pix.
= 214.016 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.836 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0122
Minimum - Maximum-0.033219367 - 0.06613168
Average (Standard dev.)0.00017563082 (±0.0018829866)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 214.016 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_50550_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_50550_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 : PDEN_2366

EntireName: PDEN_2366
Components
  • Complex: PDEN_2366
    • Protein or peptide: Aldehyde dehydrogenase
  • Ligand: POTASSIUM ION

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Supramolecule #1: PDEN_2366

SupramoleculeName: PDEN_2366 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Paracoccus denitrificans (bacteria)

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Macromolecule #1: Aldehyde dehydrogenase

MacromoleculeName: Aldehyde dehydrogenase / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: aldehyde dehydrogenase (NAD+)
Source (natural)Organism: Paracoccus denitrificans (bacteria)
Molecular weightTheoretical: 58.316895 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGHHHHHHHH HHSSGHIEGR HMPNDQTHPF RGVNALPFEE RYDNFIGGEW VAPVSGRYFT NTTPITGAEI GQIARSEAGD IELALDAAH AAKEKWGATS PAERANIMLK IADRMERNLE LLATAETWDN GKPIRETMAA DLPLAIDHFR YFAGVLRAQE G SISQIDDD ...String:
MGHHHHHHHH HHSSGHIEGR HMPNDQTHPF RGVNALPFEE RYDNFIGGEW VAPVSGRYFT NTTPITGAEI GQIARSEAGD IELALDAAH AAKEKWGATS PAERANIMLK IADRMERNLE LLATAETWDN GKPIRETMAA DLPLAIDHFR YFAGVLRAQE G SISQIDDD TVAYHFHEPL GVVGQIIPWN FPLLMACWKL APAIAAGNCV VLKPAEQTPA GIMVWANLIG DLLPPGVLNI VN GFGLEAG KPLASSNRIA KIAFTGETTT GRLIMQYASE NLIPVTLELG GKSPNIFFAD VAREDDDFFD KALEGFTMFA LNQ GEVCTC PSRVLIQESI YDKFMERAVQ RVQAIKQGDP RESDTMIGAQ ASSEQKEKIL SYLDIGKKEG AEVLTGGKAA DLGG ELSGG YYIEPTIFRG NNKMRIFQEE IFGPVVSVTT FKDQAEALEI ANDTLYGLGA GVWSRDANTC YRMGRGIKAG RVWTN CYHA YPAHAAFGGY KQSGIGRETH KMMLDHYQQT KNMLVSYSPK KLGFF

UniProtKB: Aldehyde dehydrogenase

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Macromolecule #2: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 2 / Number of copies: 2 / Formula: K
Molecular weightTheoretical: 39.098 Da

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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

Concentration0.3 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 185597
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: PROJECTION MATCHING

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