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Open data
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Basic information
Entry | Database: PDB / ID: 5xhn | ||||||
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Title | Crystal structure of Frog M-ferritin K104E mutant | ||||||
![]() | Ferritin, middle subunit | ||||||
![]() | OXIDOREDUCTASE / Ferritin / M-ferritin | ||||||
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 | ![]() ![]() | ||||||
![]() | Jagdev, M.K. / Vasudevan, D. | ||||||
![]() | ![]() Title: Surface charge dependent separation of modified and hybrid ferritin in native PAGE: Impact of lysine 104 Authors: Subhadarshanee, B. / Mohanty, A. / Jagdev, M.K. / Vasudevan, D. / Behera, R.K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 61.8 KB | Display | ![]() |
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PDB format | ![]() | 45.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 434.2 KB | Display | ![]() |
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Full document | ![]() | 435.3 KB | Display | |
Data in XML | ![]() | 12.2 KB | Display | |
Data in CIF | ![]() | 18.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5xhiC ![]() 5xhmC ![]() 5xhoC ![]() 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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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 20404.842 Da / Num. of mol.: 1 / Mutation: K104E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lithobates catesbeiana (American bullfrog) Production host: ![]() ![]() | ||||
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#2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-CL / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.33 Å3/Da / Density % sol: 63.05 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 2.0 M MgCl2 and 100 mM Bicine (pH 9.0) |
-Data collection
Diffraction | Mean temperature: 103 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 11, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.63→21.27 Å / Num. obs: 33970 / % possible obs: 100 % / Redundancy: 12.4 % / Net I/σ(I): 33.8 |
Reflection shell | Resolution: 1.63→1.66 Å / Redundancy: 11.8 % / Mean I/σ(I) obs: 5.7 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3KA3 Resolution: 1.63→21.27 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.95 / SU B: 1.188 / SU ML: 0.042 / Cross valid method: THROUGHOUT / ESU R: 0.073 / ESU R Free: 0.075 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.766 Å2
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Refinement step | Cycle: LAST / Resolution: 1.63→21.27 Å
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Refine LS restraints |
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