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- PDB-4dz0: Crystal structure of the Cu-adduct of human H-Ferritin variant MI... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4dz0 | ||||||
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Title | Crystal structure of the Cu-adduct of human H-Ferritin variant MIC1 labeled with a dansyl fluorophore | ||||||
![]() | Ferritin heavy chain | ||||||
![]() | OXIDOREDUCTASE / Four-helix bundle | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Tezcan, F.A. / Huard, D.J.E. | ||||||
![]() | ![]() Title: Re-engineering protein interfaces yields copper-inducible ferritin cage assembly. Authors: Huard, D.J. / Kane, K.M. / 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 | ![]() | 52.1 KB | Display | ![]() |
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PDB format | ![]() | 38.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 664.7 KB | Display | ![]() |
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Full document | ![]() | 664.6 KB | Display | |
Data in XML | ![]() | 8.9 KB | Display | |
Data in CIF | ![]() | 11.7 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: 20021.188 Da / Num. of mol.: 1 / Fragment: UNP residues 6-177 / Mutation: K53C, L56H, R63H, E67H, K86Q, C90E, C102A, C130A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
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#2: Chemical | ChemComp-AEN / | ||||
#3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.06 Å3/Da / Density % sol: 59.75 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 50 mM Tris, 5 mM calcium chloride, 50 mM sodium chloride, 10% PEG 3350, 350 M cupric chloride, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 23, 2011 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Rh coated flat mirror, toroidal focusing mirror Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.5→104.173 Å / Num. all: 9200 / Num. obs: 9200 / % possible obs: 100 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 20.3 % / Rsym value: 0.085 / Net I/σ(I): 26.8 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Resolution: 2.5→36.84 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.842 / SU B: 10.127 / SU ML: 0.227 / Cross valid method: THROUGHOUT / ESU R: 0.438 / ESU R Free: 0.321 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.57 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→36.84 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.565 Å / Total num. of bins used: 20
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