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- PDB-8gy3: Cryo-EM Structure of Membrane-Bound Aldehyde Dehydrogenase from G... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8gy3 | |||||||||
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Title | Cryo-EM Structure of Membrane-Bound Aldehyde Dehydrogenase from Gluconobacter oxydans | |||||||||
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Function / homology | ![]() oxidoreductase activity, acting on CH-OH group of donors / 2 iron, 2 sulfur cluster binding / ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Adachi, T. / Miyata, T. / Makino, F. / Tanaka, H. / Namba, K. / Sowa, K. / Kitazumi, Y. / Shirai, O. | |||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 262.2 KB | Display | ![]() |
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PDB format | ![]() | 211.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 34369MC ![]() 8gy2C M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
-Protein , 3 types, 3 molecules ABC
#1: Protein | ![]() Mass: 48519.500 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() References: UniProt: Q5DW50, ![]() |
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#2: Protein | Mass: 16799.998 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() References: UniProt: A0A4R4A2K3, ![]() |
#3: Protein | Mass: 83302.164 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() References: UniProt: A0A4R4A2F9, ![]() |
-Non-polymers , 4 types, 7 molecules ![](data/chem/img/HEC.gif)
![](data/chem/img/U10.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/PCD.gif)
![](data/chem/img/U10.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/PCD.gif)
#4: Chemical | ![]() #5: Chemical | ChemComp-U10 / | ![]() #6: Chemical | ![]() #7: Chemical | ChemComp-PCD / ( | ![]() |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: ![]() |
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Sample preparation
Component | Name: Aldehyde dehydrogenase from Gluconobacter oxydans![]() | |||||||||||||||||||||||||
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Molecular weight | Value: 0.15 MDa / Experimental value: YES | |||||||||||||||||||||||||
Source (natural) | Organism: ![]() | |||||||||||||||||||||||||
Source (recombinant) | Organism: ![]() | |||||||||||||||||||||||||
Buffer solution | pH: 6 | |||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 10 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied![]() ![]() | |||||||||||||||||||||||||
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 |
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Electron microscopy imaging
Microscopy | Model: JEOL CRYO ARM 300 |
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Electron gun | Electron source![]() ![]() |
Electron lens | Mode: BRIGHT FIELD![]() ![]() |
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: 12747 |
EM imaging optics | Energyfilter name![]() |
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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: 6871333 | ||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry![]() | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction![]() | Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 189414 / 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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