+Open data
-Basic information
Entry | Database: PDB / ID: 6l7i | ||||||
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Title | Signal substraction of TcdB1-TccC2 and part of TcdA1 | ||||||
Components |
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Keywords | TOXIN/PROTEIN TRANSPORT / protein transportation / TcdA1 / TcdB1 / TccC2 / TOXIN-PROTEIN TRANSPORT complex | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Photorhabdus luminescens (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å | ||||||
Authors | Yan, Z.F. / Yang, G.W. | ||||||
Citation | Journal: To Be Published Title: Signal substraction of TcdB1-TccC2 and part of TcdA1 Authors: Yan, Z.F. / Zhang, N. / Yang, G.W. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6l7i.cif.gz | 515.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6l7i.ent.gz | 431.2 KB | Display | PDB format |
PDBx/mmJSON format | 6l7i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6l7i_validation.pdf.gz | 645.1 KB | Display | wwPDB validaton report |
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Full document | 6l7i_full_validation.pdf.gz | 663 KB | Display | |
Data in XML | 6l7i_validation.xml.gz | 71.3 KB | Display | |
Data in CIF | 6l7i_validation.cif.gz | 114.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l7/6l7i ftp://data.pdbj.org/pub/pdb/validation_reports/l7/6l7i | HTTPS FTP |
-Related structure data
Related structure data | 0844MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 20255.887 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Photorhabdus luminescens (bacteria) / Gene: tcdA, tcdA1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9RN43 #2: Protein | | Mass: 165296.453 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Photorhabdus luminescens (bacteria) / Gene: tcdB1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q93EP6 #3: Protein | | Mass: 74759.125 Da / Num. of mol.: 1 / Fragment: N terminus Source method: isolated from a genetically manipulated source Source: (gene. exp.) Photorhabdus luminescens (bacteria) / Gene: TccC2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q93EP1 #4: Protein/peptide | | Mass: 1905.087 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Photorhabdus luminescens (bacteria) / Gene: TccC2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q93EP1 |
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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: Toxin complex TcdA1-TcdB1-TccC2 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: Photorhabdus luminescens (bacteria) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Microscopy | Model: FEI/PHILIPS CM300FEG/HE |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
CTF correction | Type: NONE |
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3D reconstruction | Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 124828 / Symmetry type: POINT |