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- PDB-5jkm: Binary crystal structure of positively and negatively supercharge... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5jkm | ||||||
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Title | Binary crystal structure of positively and negatively supercharged variants Ftn(pos) and Ftn(neg) from human heavy chain ferritin (Mg acetate condition) | ||||||
![]() | (Ferritin heavy ...) x 2 | ||||||
![]() | OXIDOREDUCTASE / protein design / protein engineering / charged protein containers / binary protein structures / self-assembly / binary nanoparticle superlattices | ||||||
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 | ![]() ![]() ![]() ![]() | ||||||
![]() | Kuenzle, M. / Beck, T. | ||||||
![]() | ![]() Title: Binary Protein Crystals for the Assembly of Inorganic Nanoparticle Superlattices. Authors: Kunzle, M. / Eckert, T. / 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 | ![]() | 459.1 KB | Display | ![]() |
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PDB format | ![]() | 374.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 521.7 KB | Display | ![]() |
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Full document | ![]() | 535.5 KB | Display | |
Data in XML | ![]() | 85.1 KB | Display | |
Data in CIF | ![]() | 123.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5jklSC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Ferritin heavy ... , 2 types, 12 molecules ABCDEFGHIJKL
#1: Protein | Mass: 21499.246 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 21355.549 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 4 types, 1546 molecules ![](data/chem/img/FE.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-FE / #4: Chemical | ChemComp-MG / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.81 Å3/Da / Density % sol: 56.27 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.20 M magnesium acetate, 100 mM Tris, pH 8.5, 8 mg/mL Ftn(pos) and 8 mg/mL Ftn(neg) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 15, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→47.6 Å / Num. obs: 253942 / % possible obs: 99.6 % / Redundancy: 5.65 % / Biso Wilson estimate: 18.8 Å2 / Rmerge(I) obs: 0.0628 / Net I/σ(I): 19.5 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 5.16 % / Rmerge(I) obs: 0.381 / Mean I/σ(I) obs: 3.71 / % possible all: 98.2 |
-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5JKL Resolution: 1.8→47.6 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.142 / SU ML: 0.067 / SU R Cruickshank DPI: 0.0976 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.098 / ESU R Free: 0.098 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 82.66 Å2 / Biso mean: 20.301 Å2 / Biso min: 9.94 Å2
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Refinement step | Cycle: final / Resolution: 1.8→47.6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.846 Å / Total num. of bins used: 20
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