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Yorodumi- PDB-8hnu: Cellodextrin phosphorylase stable variant from Clostridium thermo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8hnu | ||||||
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Title | Cellodextrin phosphorylase stable variant from Clostridium thermocellum | ||||||
Components | Cellodextrin phosphorylase | ||||||
Keywords | CARBOHYDRATE / cellulose / 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: 2.28 Å | ||||||
Authors | Kuga, T. / Sunagawa, N. / Igarashi, K. | ||||||
Funding support | Japan, 1items
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Citation | Journal: To Be Published Title: 11 cysteine-to-serine mutations improve the stability of cellodextrin phosphorylase 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 | 8hnu.cif.gz | 494.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8hnu.ent.gz | 322.6 KB | Display | PDB format |
PDBx/mmJSON format | 8hnu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8hnu_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 8hnu_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 8hnu_validation.xml.gz | 67.2 KB | Display | |
Data in CIF | 8hnu_validation.cif.gz | 102.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hn/8hnu ftp://data.pdbj.org/pub/pdb/validation_reports/hn/8hnu | HTTPS FTP |
-Related structure data
Related structure data | 34918MC 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: 112736.172 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acetivibrio thermocellus (bacteria) / Strain: YM4 / Gene: cdp-ym4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q93HT8 #2: Chemical | ChemComp-CL / #3: Water | ChemComp-HOH / | 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: cellodextrin phosphorylase dimer / 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) |
Buffer solution | pH: 7.5 |
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 |
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: 9582559 | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.28 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 998544 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 99.59 Å2 | ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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