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- PDB-8pp2: Binary crystal structure of positively supercharged ferritin vari... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8pp2 | ||||||
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Title | Binary crystal structure of positively supercharged ferritin variant Ftn(pos) and native(K86Q) human heavy chain ferritin (Mg formate condition) | ||||||
![]() | (Ferritin heavy chain, N-terminally ...) x 2 | ||||||
![]() | OXIDOREDUCTASE / protein design / charged protein container / binary protein structures / self-assembly / binary nanocage assembly | ||||||
Function / homology | ![]() iron ion sequestering activity / : / autolysosome / Scavenging by Class A Receptors / Golgi Associated Vesicle Biogenesis / ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / negative regulation of fibroblast proliferation / ferric iron binding ...iron ion sequestering activity / : / autolysosome / Scavenging by Class A Receptors / Golgi Associated Vesicle Biogenesis / ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / negative regulation of fibroblast proliferation / ferric iron binding / Iron uptake and transport / ferrous iron binding / tertiary granule lumen / iron ion transport / intracellular iron ion homeostasis / ficolin-1-rich granule lumen / iron ion binding / immune response / negative regulation of cell population proliferation / Neutrophil degranulation / extracellular exosome / extracellular region / identical protein binding / membrane / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lang, L. / Beck, T. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Assembly Requirements for the Construction of Large-Scale Binary Protein Structures. Authors: Lang, L. / Bohler, H. / Wagler, H. / Beck, T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 828 KB | Display | ![]() |
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PDB format | ![]() | 672.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 528.7 KB | Display | ![]() |
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Full document | ![]() | 544.4 KB | Display | |
Data in XML | ![]() | 75.6 KB | Display | |
Data in CIF | ![]() | 106.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8pp3C ![]() 8pp4C ![]() 8pp5C C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Ferritin heavy chain, N-terminally ... , 2 types, 12 molecules ABCDEFGHIJKL
#1: Protein | Mass: 20360.135 Da / Num. of mol.: 6 Mutation: K86Q, A18K, C90K, N98R, C102K, H105K, N25R, N109K, D123K, E162R Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 20115.494 Da / Num. of mol.: 6 / Mutation: K86Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 4 types, 723 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-FE / #5: Chemical | ChemComp-MG / #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: reservoir: 0.19M Magnesium Formate Ftn(pos): 4 mg/mL in 50mM Tris pH 7.5 1 M NaCl Ftn(Wildtype): 4mg/mL in 50mM Tris pH 7.5 0.3 M NaCl 2 uL reservoir + 1uL Ftn(pos) + 1uL Ftn(Wildtype) added ...Details: reservoir: 0.19M Magnesium Formate Ftn(pos): 4 mg/mL in 50mM Tris pH 7.5 1 M NaCl Ftn(Wildtype): 4mg/mL in 50mM Tris pH 7.5 0.3 M NaCl 2 uL reservoir + 1uL Ftn(pos) + 1uL Ftn(Wildtype) added to coverslide in this order. |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: nitrogen cryostream / Serial crystal experiment: N | |||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 7, 2020 | |||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 2→49.061 Å / Num. obs: 186148 / % possible obs: 99.9 % / Redundancy: 13.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.173 / Rpim(I) all: 0.07 / Rrim(I) all: 0.187 / Net I/σ(I): 10.2 | |||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.915 Å2
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Refinement step | Cycle: LAST / Resolution: 2.001→49.061 Å
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Refine LS restraints |
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LS refinement shell |
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