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Yorodumi- PDB-8gy2: Cryo-EM Structure of Membrane-Bound Alcohol Dehydrogenase from Gl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8gy2 | |||||||||
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Title | Cryo-EM Structure of Membrane-Bound Alcohol Dehydrogenase from Gluconobacter oxydans | |||||||||
Components |
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Keywords | OXIDOREDUCTASE / Complex / Oxidereductase / Membrane-bound protein | |||||||||
Function / homology | Function and homology information alcohol dehydrogenase (quinone) / oxidoreductase activity, acting on CH-OH group of donors / : / outer membrane-bounded periplasmic space / electron transfer activity / iron ion binding / calcium ion binding / heme binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Gluconobacter oxydans 621H (bacteria) Gluconobacter oxydans (bacteria) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.5 Å | |||||||||
Authors | Adachi, T. / Miyata, T. / Makino, F. / Tanaka, H. / Namba, K. / Sowa, K. / Kitazumi, Y. / Shirai, O. | |||||||||
Funding support | Japan, 2items
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Citation | Journal: Acs Catalysis / Year: 2023 Title: Experimental and Theoretical Insights into Bienzymatic Cascade for Mediatorless Bioelectrochemical Ethanol Oxidation with Alcohol and Aldehyde Dehydrogenases Authors: Adachi, T. / Miyata, T. / Makino, F. / Tanaka, H. / Namba, K. / Kano, K. / Sowa, K. / Kitazumi, Y. / Shirai, O. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8gy2.cif.gz | 253.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8gy2.ent.gz | 204.2 KB | Display | PDB format |
PDBx/mmJSON format | 8gy2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8gy2_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 8gy2_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 8gy2_validation.xml.gz | 53.2 KB | Display | |
Data in CIF | 8gy2_validation.cif.gz | 77.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gy/8gy2 ftp://data.pdbj.org/pub/pdb/validation_reports/gy/8gy2 | HTTPS FTP |
-Related structure data
Related structure data | 34368MC 8gy3C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Alcohol dehydrogenase (quinone), ... , 2 types, 2 molecules AB
#1: Protein | Mass: 82938.906 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gluconobacter oxydans 621H (bacteria) / Strain: 621H / Gene: adhA, GOX1068 / Production host: Gluconobacter oxydans (bacteria) References: UniProt: O05542, alcohol dehydrogenase (quinone) |
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#2: Protein | Mass: 51249.598 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gluconobacter oxydans 621H (bacteria) / Strain: 621H / Gene: adhB, GOX1067 / Production host: Gluconobacter oxydans (bacteria) References: UniProt: Q47945, alcohol dehydrogenase (quinone) |
-Protein , 1 types, 1 molecules C
#3: Protein | Mass: 14282.063 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gluconobacter oxydans (bacteria) / Production host: Gluconobacter oxydans (bacteria) References: UniProt: O05544, alcohol dehydrogenase (quinone) |
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-Non-polymers , 4 types, 7 molecules
#4: Chemical | ChemComp-HEC / #5: Chemical | ChemComp-PQQ / | #6: Chemical | ChemComp-CA / | #7: Chemical | ChemComp-U10 / | |
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-Details
Has ligand of interest | N |
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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: Alcohol dehydrogenase from Gluconobacter oxydans / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT | |||||||||||||||||||||||||
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Molecular weight | Value: 0.15 MDa / Experimental value: YES | |||||||||||||||||||||||||
Source (natural) | Organism: Gluconobacter oxydans (bacteria) | |||||||||||||||||||||||||
Source (recombinant) | Organism: Gluconobacter oxydans (bacteria) | |||||||||||||||||||||||||
Buffer solution | pH: 6 | |||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 10 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3 | |||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Microscopy | Model: JEOL CRYO ARM 300 |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 60000 X / Calibrated magnification: 56754 X / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm / Calibrated defocus min: 500 nm / Calibrated defocus max: 2500 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: JEOL CRYOSPECPORTER / Temperature (max): 80 K / Temperature (min): 80 K / Residual tilt: 0.01 mradians |
Image recording | Average exposure time: 3 sec. / Electron dose: 2 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 3224 |
EM imaging optics | Energyfilter name: In-column Omega Filter / Energyfilter slit width: 20 eV |
-Processing
Software | Name: PHENIX / Version: 1.20.1_4487: / 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: 2551393 | ||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 247480 / Algorithm: BACK PROJECTION / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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