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Yorodumi- PDB-6k4m: Cryo-EM structure of Holo-bacterioferritin form-II from Streptomy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6k4m | ||||||
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Title | Cryo-EM structure of Holo-bacterioferritin form-II from Streptomyces coelicolor | ||||||
Components | Bacterioferritin | ||||||
Keywords | METAL TRANSPORT / Ferritin / Nanocage / Bacterioferritin | ||||||
Function / homology | Function and homology information 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 | Streptomyces coelicolor (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.5 Å | ||||||
Authors | Jobichen, C. / Sivaraman, J. | ||||||
Citation | Journal: To Be Published Title: Cryo-EM structure of Bacterioferritin from Streptomyces coelicolor Authors: Jobichen, C. / Sivaraman, J. | ||||||
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 | 6k4m.cif.gz | 670.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6k4m.ent.gz | 570.4 KB | Display | PDB format |
PDBx/mmJSON format | 6k4m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6k4m_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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Full document | 6k4m_full_validation.pdf.gz | 2 MB | Display | |
Data in XML | 6k4m_validation.xml.gz | 107.5 KB | Display | |
Data in CIF | 6k4m_validation.cif.gz | 152.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k4/6k4m ftp://data.pdbj.org/pub/pdb/validation_reports/k4/6k4m | HTTPS FTP |
-Related structure data
Related structure data | 9915MC 9910C 9913C 6k3oC 6k43C C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-Links
-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.) Streptomyces coelicolor (bacteria) Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) Strain (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 |
-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: Streptomyces coelicolor (bacteria) |
Source (recombinant) | Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) 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. |
Vitrification | Cryogen name: ETHANE |
-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: OTHER |
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) |
-Processing
Software | Name: PHENIX / Version: 1.14_3260: / 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: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 13793 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT | ||||||||||||||||||||||||
Atomic model building | PDB-ID: 5XX9 Accession code: 5XX9 / Source name: PDB / Type: experimental model | ||||||||||||||||||||||||
Refine LS restraints |
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