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Yorodumi- PDB-8h6h: cryo-EM structure of cellodextrin phosphorylase from Clostridium ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8h6h | |||||||||
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Title | cryo-EM structure of cellodextrin phosphorylase from Clostridium thermocellum | |||||||||
Components | Cellodextrin phosphorylase | |||||||||
Keywords | CARBOHYDRATE / cellulose / cellodextrin / phosphorolysis / synthesis | |||||||||
Function / homology | Function and homology information glycosyltransferase activity / carbohydrate binding / carbohydrate metabolic process Similarity search - Function | |||||||||
Biological species | Acetivibrio thermocellus (bacteria) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.3 Å | |||||||||
Authors | Kuga, T. / Sunagawa, N. / Igarashi, K. | |||||||||
Funding support | Japan, 2items
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Citation | Journal: To Be Published Title: structure and dynamics of cellodextrin phosphorylase from Clostridium thermocellum determine chain length and crystalline packing of highly ordered cellulose II synthesized in vitro Authors: 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 | 8h6h.cif.gz | 720.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8h6h.ent.gz | 603.3 KB | Display | PDB format |
PDBx/mmJSON format | 8h6h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8h6h_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 8h6h_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 8h6h_validation.xml.gz | 65.3 KB | Display | |
Data in CIF | 8h6h_validation.cif.gz | 99.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h6/8h6h ftp://data.pdbj.org/pub/pdb/validation_reports/h6/8h6h | HTTPS FTP |
-Related structure data
Related structure data | 34504MC 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: 112599.523 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acetivibrio thermocellus (bacteria) / Gene: cdp-ym4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q93HT8 #2: Chemical | ChemComp-CL / 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: Homodimeric structure of cellodextrin phosphorylase from Clostridium thermocellum (CtCDP) Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT | ||||||||||||||||||||
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Molecular weight | Value: 0.24 MDa / Experimental value: YES | ||||||||||||||||||||
Source (natural) | Organism: Acetivibrio thermocellus (bacteria) / Strain: YM4 | ||||||||||||||||||||
Source (recombinant) | Organism: Escherichia coli (E. coli) / Strain: BL21 (DE3) / Plasmid: pET28-b | ||||||||||||||||||||
Buffer solution | pH: 7.5 / Details: 20 mM Tris-HCl, 120 mM NaCl, 0.1 mM DTT | ||||||||||||||||||||
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: 280 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 |
Image recording | Electron dose: 49 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software |
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 3503460 | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 604474 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 86.98 Å2 | ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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