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Yorodumi- PDB-8iyr: The cryo-EM structure of cellobiose phosphorylase from Clostridiu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8iyr | ||||||
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Title | The cryo-EM structure of cellobiose phosphorylase from Clostridium thermocellum in complex with phosphate | ||||||
Components | Cellobiose phosphorylase | ||||||
Keywords | TRANSFERASE / Cellobiose phosphorylase | ||||||
Function / homology | Function and homology information cellobiose phosphorylase / cellobiose phosphorylase activity / cellulose catabolic process / carbohydrate binding Similarity search - Function | ||||||
Biological species | Acetivibrio thermocellus (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.6 Å | ||||||
Authors | Iriya, S. / Kuga, T. / Sunagawa, N. / Igarashi, K. | ||||||
Funding support | Japan, 1items
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Citation | Journal: To Be Published Title: The cryo-EM structure of cellobiose phosphorylase from Clostridium thermocellum in complex with phosphate Authors: Iriya, S. / Kuga, T. / Sunagawa, N. / Igarashi, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8iyr.cif.gz | 402.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8iyr.ent.gz | 263.3 KB | Display | PDB format |
PDBx/mmJSON format | 8iyr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8iyr_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 8iyr_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 8iyr_validation.xml.gz | 55 KB | Display | |
Data in CIF | 8iyr_validation.cif.gz | 80.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iy/8iyr ftp://data.pdbj.org/pub/pdb/validation_reports/iy/8iyr | HTTPS FTP |
-Related structure data
Related structure data | 35829MC 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
#1: Protein | Mass: 93872.453 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acetivibrio thermocellus (bacteria) / Strain: YM4 / Gene: cbp / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8VP44, cellobiose phosphorylase #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: cellobiose phosphorylase / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT | |||||||||||||||
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Molecular weight | Value: 0.18 MDa / Experimental value: NO | |||||||||||||||
Source (natural) | Organism: Acetivibrio thermocellus (bacteria) / Strain: YM4 | |||||||||||||||
Source (recombinant) | Organism: Escherichia coli BL21(DE3) (bacteria) / Plasmid: pET28 | |||||||||||||||
Buffer solution | pH: 6.5 / Details: 20 mM BisTris-HCl, 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 |
-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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Average exposure time: 5.35 sec. / Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 3447 |
-Processing
Software |
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EM software |
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CTF correction | Type: NONE | ||||||||||||||||||||||||
Particle selection | Num. of particles selected: 781500 | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 463540 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.81 Å2 | ||||||||||||||||||||||||
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