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- PDB-8hob: The cryo-EM structure of cellobiose phosphorylase from Clostridiu... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8hob | ||||||
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Title | The cryo-EM structure of cellobiose phosphorylase from Clostridium thermocellum ( variant) | ||||||
![]() | Cellobiose phosphorylase | ||||||
![]() | TRANSFERASE / Cellobiose phosphorylase | ||||||
Function / homology | ![]() cellobiose phosphorylase / cellobiose phosphorylase activity / carbohydrate binding / carbohydrate metabolic process Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.19 Å | ||||||
![]() | Iriya, S. / Kuga, T. / Sunagawa, N. / Igarashi, K. | ||||||
Funding support | ![]()
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![]() | ![]() Title: The cryo-EM structure of cellobiose phosphorylase from Clostridium thermocellum Authors: Iriya, S. / Kuga, T. / Sunagawa, N. / Igarashi, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 329.3 KB | Display | ![]() |
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PDB format | ![]() | 266.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 58.6 KB | Display | |
Data in CIF | ![]() | 89 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 34924MC ![]() 8ho7C ![]() 8ho9C C: citing same article ( M: map data used to model this data |
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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
#1: Protein | Mass: 93973.258 Da / Num. of mol.: 2 / Mutation: cysteine-to-serine variant Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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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 |
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Sample preparation
Component | Name: Cellobiose phosphorylase / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: RECOMBINANT | |||||||||||||||
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Molecular weight | Value: 0.18 MDa / Experimental value: YES | |||||||||||||||
Source (natural) | Organism: ![]() | |||||||||||||||
Source (recombinant) | Organism: ![]() ![]() | |||||||||||||||
Buffer solution | pH: 6.5 / Details: 20 mM MES, 70 mM NaCl | |||||||||||||||
Buffer component |
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Specimen | Conc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 | |||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 279 K / Details: Vitrification carried out in nitrogen atmosphere. |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 1800 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm |
Image recording | Average exposure time: 5.567 sec. / Electron dose: 49 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 3744 |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 2976880 | ||||||||||||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.19 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1070321 / Symmetry type: POINT |