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Open data
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Basic information
Entry | Database: PDB / ID: 4lqh | ||||||
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Title | High resolution structure of native 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 | Rana 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 | ![]() | 99.3 KB | Display | ![]() |
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PDB format | ![]() | 77.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 425.5 KB | Display | ![]() |
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Full document | ![]() | 426.3 KB | Display | |
Data in XML | ![]() | 12.7 KB | Display | |
Data in CIF | ![]() | 20 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4lpjC ![]() 4lqjC ![]() 4lqvC ![]() 4lyuC ![]() 4lyxC ![]() 4mjyC ![]() 4mkuC ![]() 4ml5C ![]() 4mn9C ![]() 4my7C ![]() 6i36C ![]() 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.) Rana 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: 3.17 Å3/Da / Density % sol: 61.17 % |
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Crystal grow | Temperature: 298 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 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 18, 2012 / Details: mirror | |||||||||||||||||||||
Radiation | Monochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 1.2399 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 1.16→21.73 Å / Num. all: 515592 / Num. obs: 86036 / % possible obs: 92.8 % / Observed criterion σ(I): 2 / Redundancy: 6 % / Biso Wilson estimate: 9.634 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 12.7 | |||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: pdb entry 3KA3 Resolution: 1.16→21.73 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.972 / SU B: 0.719 / SU ML: 0.017 / Cross valid method: THROUGHOUT / σ(I): 2 / ESU R: 0.031 / ESU R Free: 0.03 / 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: 11.615 Å2
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Refinement step | Cycle: LAST / Resolution: 1.16→21.73 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.158→1.188 Å / Total num. of bins used: 20
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