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- PDB-6k3o: Cryo-EM structure of Apo-bacterioferritin from Streptomyces coelicolor -
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Open data
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Basic information
Entry | Database: PDB / ID: 6k3o | ||||||
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Title | Cryo-EM structure of Apo-bacterioferritin from Streptomyces coelicolor | ||||||
![]() | Bacterioferritin | ||||||
![]() | METAL TRANSPORT / Ferritin / Nanocage / Bacterioferritin | ||||||
Function / homology | ![]() ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / ferric iron binding / iron ion transport / iron ion binding / heme binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å | ||||||
![]() | Jobichen, C. / Sivaraman, J. | ||||||
![]() | ![]() Title: Cryo-EM structure of Apo-bacterioferritin from Streptomyces coelicolor. Authors: Jobichen, C. / Sivaraman, J. | ||||||
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 668.5 KB | Display | ![]() |
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PDB format | ![]() | 565.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.9 MB | Display | ![]() |
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Full document | ![]() | 2 MB | Display | |
Data in XML | ![]() | 113.4 KB | Display | |
Data in CIF | ![]() | 156.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 9910MC ![]() 9913C ![]() 9915C ![]() 6k43C ![]() 6k4mC M: map data used to model this data C: citing same article ( |
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Similar structure data | |
Experimental dataset #1 | Data reference: ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 19242.629 Da / Num. of mol.: 24 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() Variant (production host): 'BL21-Gold(DE3)pLysS AG' / References: UniProt: Q9S2N0, ferroxidase #2: Chemical | ChemComp-FE2 / #3: Chemical | ChemComp-HEM / |
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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 |
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Sample preparation
Component | Name: Bacterioferritin in complex with HEME and IRON / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: RECOMBINANT |
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Molecular weight | Value: 0.5 MDa / Experimental value: YES |
Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() ![]() Strain: 'BL21-Gold(DE3)pLysS AG' |
Buffer solution | pH: 7 |
Specimen | Conc.: 1.8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: This sample was monodisperse with 24mer nanocage assemblies. |
Specimen support | Grid material: GOLD / Grid type: Quantifoil, UltrAuFoil, R1.2/1.3 |
Vitrification | Cryogen name: ETHANE |
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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: ![]() |
Electron lens | Mode: BRIGHT FIELD / C2 aperture diameter: 2.7 µm |
Image recording | Electron dose: 1.6 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) |
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Processing
Software | Name: PHENIX / Version: 1.15.2_3472: / Classification: refinement | ||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: O (octahedral) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 77066 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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