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- PDB-8pp5: Unitary crystal structure of positively supercharged ferritin var... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8pp5 | ||||||
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Title | Unitary crystal structure of positively supercharged ferritin variant Ftn(pos)-m1 (Mg Formate condition) | ||||||
![]() | Ferritin heavy chain, N-terminally processed | ||||||
![]() | OXIDOREDUCTASE / protein design / protein engineering / protein interfaces / superlattice / nanocage / ferritin / protein container / charged nanocage | ||||||
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 | ![]() | 438.3 KB | Display | ![]() |
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PDB format | ![]() | 352.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 458 KB | Display | ![]() |
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Full document | ![]() | 459.8 KB | Display | |
Data in XML | ![]() | 45.1 KB | Display | |
Data in CIF | ![]() | 66.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8pp2C ![]() 8pp3C ![]() 8pp4C 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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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 20302.033 Da / Num. of mol.: 6 Mutation: C90K, N98R, C102K, H105K N25R, N109K, D123K, E162R Source method: isolated from a genetically manipulated source Details: Ftn-pos-m1, positively charged human heavy chain ferritin with one crystal contact mutation reverted. Source: (gene. exp.) ![]() Production host: ![]() ![]() Strain (production host): BL21-Gold / References: UniProt: P02794 #2: Chemical | ChemComp-FE / #3: Chemical | ChemComp-MG / #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.1 Å3/Da / Density % sol: 60.29 % |
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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)-m1: 4 mg/mL in 50mM Tris pH 7.5 0.9 M NaCl 2microliter reservoir + 1microliter Ftn(pos)-m1 +1 microliterL 50mM Tris pH 7.5 0.3 M NaCl Temp details: held constant |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: Cryostream / Serial crystal experiment: N | |||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 13, 2021 | |||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 1.75→105.09 Å / Num. obs: 145913 / % possible obs: 98.9 % / Redundancy: 10.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.174 / Rpim(I) all: 0.082 / Rrim(I) all: 0.193 / Net I/σ(I): 8.3 | |||||||||||||||||||||
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: 26.449 Å2
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Refinement step | Cycle: LAST / Resolution: 2→105.086 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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