+Open data
-Basic information
Entry | Database: PDB / ID: 8qhs | ||||||
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Title | Cryo-EM structure of the monocin tail-tube, MttP. | ||||||
Components | Antigen A | ||||||
Keywords | TOXIN / Listeria / monocytogenes / tailocins | ||||||
Function / homology | Phage major tail protein TP901-1 / Phage tail tube protein / Antigen A Function and homology information | ||||||
Biological species | Listeria monocytogenes 10403S (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.3 Å | ||||||
Authors | Nadejda, S. / Lichtenstein, R. / Schlussel, S. / Azulay, G. / Borovok, I. / Holdengraber, V. / Elad, N. / Wolf, S.G. / Zalk, R. / Zarivach, R. ...Nadejda, S. / Lichtenstein, R. / Schlussel, S. / Azulay, G. / Borovok, I. / Holdengraber, V. / Elad, N. / Wolf, S.G. / Zalk, R. / Zarivach, R. / Frank, G.A. / Herskovits, A.A. | ||||||
Funding support | European Union, 1items
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Citation | Journal: To Be Published Title: Tailocin cell factories Authors: Nadejda, S. / Lichtenstein, R. / Schlussel, S. / Azulay, G. / Borovok, I. / Holdengraber, V. / Elad, N. / Wolf, S.G. / Zalk, R. / Zarivach, R. / Frank, G.A. / Herskovits, A.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8qhs.cif.gz | 144.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8qhs.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8qhs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8qhs_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 8qhs_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 8qhs_validation.xml.gz | 41 KB | Display | |
Data in CIF | 8qhs_validation.cif.gz | 57.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qh/8qhs ftp://data.pdbj.org/pub/pdb/validation_reports/qh/8qhs | HTTPS FTP |
-Related structure data
Related structure data | 18416MC 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: 18010.260 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Listeria monocytogenes 10403S (bacteria) Gene: LMRG_02367 / Production host: Listeria monocytogenes 10403S (bacteria) / References: UniProt: A0A0H3GGY8 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: HELICAL ARRAY / 3D reconstruction method: helical reconstruction |
-Sample preparation
Component | Name: Listeria monocytogenes 10403S monocin tail tube comprised of LMRG_02367 tail tube protein (MttP) Type: COMPLEX / Entity ID: #1 / Source: NATURAL |
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Molecular weight | Value: 1 kDa/nm / Experimental value: NO |
Source (natural) | Organism: Listera (plant) |
Buffer solution | pH: 7 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Cryogen name: ETHANE / Humidity: 30 % / Chamber temperature: 20 K / Details: Homemade pneumatic apparatus |
-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: 2000 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 2 sec. / Electron dose: 49.5 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 15 eV |
Image scans | Movie frames/image: 50 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||
Helical symmerty | Angular rotation/subunit: 25.078 ° / Axial rise/subunit: 39.297 Å / Axial symmetry: C6 | |||||||||||||||||||||||||
Particle selection | Num. of particles selected: 503874 | |||||||||||||||||||||||||
3D reconstruction | Resolution: 2.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 490830 / Algorithm: FOURIER SPACE / Symmetry type: HELICAL | |||||||||||||||||||||||||
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