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Open data
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Basic information
Entry | Database: PDB / ID: 6i36 | |||||||||
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Title | SIXTY MINUTES IRON LOADED FROG M FERRITIN | |||||||||
![]() | Ferritin, middle subunit | |||||||||
![]() | OXIDOREDUCTASE / FOUR HELIX BUNDLE / FERROXIDASE | |||||||||
Function / homology | ![]() ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / ferric iron binding / ferrous iron binding / iron ion transport / cytoplasm Similarity search - Function | |||||||||
Biological species | Lithobates catesbeiana (American bullfrog) | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Mangani, S. / Di Pisa, F. / Pozzi, C. / Turano, P. / Lalli, D. | |||||||||
![]() | ![]() Title: Time-Lapse Anomalous X-Ray Diffraction Shows How Fe(2+) Substrate Ions Move Through Ferritin Protein Nanocages To Oxidoreductase Sites. Authors: Pozzi, C. / Di Pisa, F. / Lalli, D. / Rosa, C. / Theil, E. / Turano, P. / Mangani, S. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 63.7 KB | Display | ![]() |
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PDB format | ![]() | 45.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 416.1 KB | Display | ![]() |
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Full document | ![]() | 416 KB | Display | |
Data in XML | ![]() | 12.5 KB | Display | |
Data in CIF | ![]() | 19.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4lpjC ![]() 4lqhC ![]() 4lqjC ![]() 4lqvC ![]() 4lyuC ![]() 4lyxC ![]() 4mjyC ![]() 4mkuC ![]() 4ml5C ![]() 4mn9C ![]() 4my7C ![]() 3ka3S C: citing same article ( S: Starting model for refinement |
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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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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 20623.182 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lithobates catesbeiana (American bullfrog) Production host: ![]() ![]() | ||||||
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#2: Chemical | ChemComp-FE2 / #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-CL / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.16 Å3/Da / Density % sol: 61.04 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 1.6-2M MAGNESIUM CHLORIDE, 0.1M BICINE, pH 9.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K PH range: 9 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 3, 2012 / Details: MIRROR | ||||||||||||
Radiation | Monochromator: Si111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.59→19.64 Å / Num. obs: 36091 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 5.8 % / Biso Wilson estimate: 12.42 Å2 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.051 / Rrim(I) all: 0.13 / Net I/σ(I): 7.2 | ||||||||||||
Reflection shell | Resolution: 1.59→1.68 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.275 / Mean I/σ(I) obs: 3.4 / Rpim(I) all: 0.154 / Rrim(I) all: 0.343 / % possible all: 98.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3KA3 Resolution: 1.59→19.64 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.941 / SU B: 1.232 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.081 / ESU R Free: 0.077
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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 mean: 11.65 Å2
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Refine analyze | Luzzati coordinate error obs: 0.18 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.59→19.64 Å
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Refine LS restraints |
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