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Open data
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Basic information
Entry | Database: PDB / ID: 7die | ||||||
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Title | Crystal structure of M. penetrans Ferritin | ||||||
![]() | Ferritin | ||||||
![]() | METAL BINDING PROTEIN / Ferritin / Iron uptake / Iron release. | ||||||
Function / homology | ![]() bacterial non-heme ferritin / ferric iron binding / iron ion transport / intracellular iron ion homeostasis / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wang, w.m. / Zhang, y. / Wang, h.f. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Ferritin with Atypical Ferroxidase Centers Takes B-Channels as the Pathway for Fe 2+ Uptake from Mycoplasma . Authors: Wang, W. / Zhang, Y. / Zhao, G. / Wang, H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 226.6 KB | Display | ![]() |
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PDB format | ![]() | 182 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 13 MB | Display | ![]() |
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Full document | ![]() | 13 MB | Display | |
Data in XML | ![]() | 42.6 KB | Display | |
Data in CIF | ![]() | 62.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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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: 20663.520 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: HF-2 / Gene: MYPE2930 / Production host: ![]() ![]() #2: Chemical | ChemComp-FE / #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.89 Å3/Da / Density % sol: 57.46 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.2 M ammonium acetate, 0.1 M Tris-HCl (pH 8.5), 10-15% (w/v) MPD |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 17, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 110615 / % possible obs: 99.7 % / Redundancy: 6.9 % / CC1/2: 0.992 / Rpim(I) all: 0.041 / Rrim(I) all: 0.108 / Χ2: 1.609 / Net I/σ(I): 30.79 |
Reflection shell | Resolution: 1.9→1.93 Å / Mean I/σ(I) obs: 3.875 / Num. unique obs: 5458 / CC1/2: 0.927 / CC star: 0.981 / Rpim(I) all: 0.174 / Rrim(I) all: 0.463 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 105.4 Å2 / Biso mean: 33.904 Å2 / Biso min: 21.17 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.9→47.856 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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