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- PDB-9ldl: The complex structure of Halomonas eurihalina BdhE -

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Basic information

Entry
Database: PDB / ID: 9ldl
TitleThe complex structure of Halomonas eurihalina BdhE
ComponentsAldehyde dehydrogenase family protein
KeywordsBIOSYNTHETIC PROTEIN / Complex / Enzyme
Function / homology
Function and homology information


oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor / metal ion binding
Similarity search - Function
Iron-containing alcohol dehydrogenases signature 2. / : / Fe-containing alcohol dehydrogenase family, C-terminal / Iron-containing alcohol dehydrogenases signature 1. / Alcohol dehydrogenase, iron-type, conserved site / Alcohol dehydrogenase, iron-type/glycerol dehydrogenase GldA / Iron-containing alcohol dehydrogenase / Aldehyde dehydrogenase, glutamic acid active site / Aldehyde dehydrogenases glutamic acid active site. / Aldehyde dehydrogenase domain ...Iron-containing alcohol dehydrogenases signature 2. / : / Fe-containing alcohol dehydrogenase family, C-terminal / Iron-containing alcohol dehydrogenases signature 1. / Alcohol dehydrogenase, iron-type, conserved site / Alcohol dehydrogenase, iron-type/glycerol dehydrogenase GldA / Iron-containing alcohol dehydrogenase / Aldehyde dehydrogenase, glutamic acid active site / Aldehyde dehydrogenases glutamic acid 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 family protein
Similarity search - Component
Biological speciesHalomonas eurihalina (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.55 Å
AuthorsKonno, N. / Miyake, K. / Nishino, S. / Omae, K. / Yanagisawa, H. / Tsuru, S. / Kikkawa, M. / Furusawa, C. / Iwasaki, W.
Funding support Japan, 6items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)22J20318 Japan
Japan Society for the Promotion of Science (JSPS)24H00870 Japan
Japan Society for the Promotion of Science (JSPS)21H05247 Japan
Japan Society for the Promotion of Science (JSPS)21H05248 Japan
Japan Science and TechnologyJPMJER1902 Japan
Japan Agency for Medical Research and Development (AMED)JP24ama121002 Japan
CitationJournal: To Be Published
Title: Repeatability of protein structural evolution following convergent gene fusions
Authors: Konno, N. / Miyake, K. / Nishino, S. / Omae, K. / Yanagisawa, H. / Tsuru, S. / Kikkawa, M. / Furusawa, C. / Iwasaki, W.
History
DepositionJan 6, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 1, 2025Provider: repository / Type: Initial release
Revision 1.0Oct 1, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Oct 1, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 1, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 1, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Oct 1, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: Aldehyde dehydrogenase family protein
A: Aldehyde dehydrogenase family protein
B: Aldehyde dehydrogenase family protein
D: Aldehyde dehydrogenase family protein


Theoretical massNumber of molelcules
Total (without water)377,8774
Polymers377,8774
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Aldehyde dehydrogenase family protein


Mass: 94469.305 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Halomonas eurihalina (bacteria) / Gene: FZZ93_11685 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A5D9D7B4
Has protein modificationN

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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: A tetrameric complex of BdhE / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.377 MDa / Experimental value: NO
Source (natural)Organism: Halomonas eurihalina (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 1.35
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMTris-HCl (pH 8.0)1
2100 mMSodium chlorideNaCl1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Circular tetramer
Specimen supportGrid material: COPPER
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 279 K

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Electron microscopy imaging

MicroscopyModel: TFS TALOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1750 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.55 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 667288 / Symmetry type: POINT

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