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- PDB-6b8g: Twice-Contracted Human Heavy-Chain Ferritin Crystal-Hydrogel Hybrid -
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Open data
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Basic information
Entry | Database: PDB / ID: 6b8g | ||||||
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Title | Twice-Contracted Human Heavy-Chain Ferritin Crystal-Hydrogel Hybrid | ||||||
![]() | Ferritin heavy chain | ||||||
![]() | OXIDOREDUCTASE / Hydrogel / Polymer | ||||||
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 | ![]() ![]() | ||||||
![]() | Zhang, L. / Bailey, J.B. / Subramanian, R. / Tezcan, F.A. | ||||||
![]() | ![]() Title: Hyperexpandable, self-healing macromolecular crystals with integrated polymer networks. Authors: Zhang, L. / Bailey, J.B. / Subramanian, R.H. / Tezcan, F.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 151.9 KB | Display | ![]() |
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PDB format | ![]() | 123.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 426 KB | Display | ![]() |
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Full document | ![]() | 427.6 KB | Display | |
Data in XML | ![]() | 13.6 KB | Display | |
Data in CIF | ![]() | 21.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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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
#1: Protein | Mass: 21085.248 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
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#2: Chemical | #3: Chemical | ChemComp-CA / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.02 Å3/Da / Density % sol: 59.31 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: Reservoir: 500 uL of 25 mM HEPES pH 7.0 with 10 mM CaCl2 Well: 2 uL of reservoir solution and 2 uL of 2.5 uM ferritin (by 24-mer) in 15 mM TRIS pH 7.4 with 150 mM NaCl After crystals formed, ...Details: Reservoir: 500 uL of 25 mM HEPES pH 7.0 with 10 mM CaCl2 Well: 2 uL of reservoir solution and 2 uL of 2.5 uM ferritin (by 24-mer) in 15 mM TRIS pH 7.4 with 150 mM NaCl After crystals formed, a crystal was harvested and soaked in a buffered solution comprised of 25 mM HEPES pH 7.0, 30 mM CaCl2, 8.6 % (w/v) sodium acrylate, 2.5 % (w/v) acrylamide, and 0.2 % (w/v) Bis-acrylamide overnight. Crystal was transferred to a solution containing 1 % APS and 1% TEMED with 4 M NaCl for 5 min. Crystal was then transferred to a clean slide and soaked in 30 uL H2O for 5 min. The H2O was removed the crystal was soaked in 4 M NaCl for 2 min. The crystal was removed, and soaked in 30 uL H2O for 5 min. This solution was removed and the crystal was soaked in 1 M CaCl2 for 2 min. The crystal was removed, cryoprotected in perfluoro polyether, and frozen in liquid N2. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 22, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 1.13→63.62 Å / Num. obs: 92912 / % possible obs: 100 % / Redundancy: 32.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.131 / Net I/σ(I): 19.1 |
Reflection shell | Resolution: 1.13→1.15 Å / Redundancy: 13.8 % / Rmerge(I) obs: 1.131 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 4518 / CC1/2: 0.628 / % possible all: 100 |
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Processing
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Refinement | Resolution: 1.13→34.631 Å / SU ML: 0.09 / σ(F): 1.34 / Phase error: 9.11 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.13→34.631 Å
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Refine LS restraints |
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LS refinement shell |
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