+Open data
-Basic information
Entry | Database: PDB / ID: 5xhn | ||||||
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Title | Crystal structure of Frog M-ferritin K104E mutant | ||||||
Components | Ferritin, middle subunit | ||||||
Keywords | OXIDOREDUCTASE / Ferritin / M-ferritin | ||||||
Function / homology | Function and homology information ferroxidase / ferroxidase activity / intracellular sequestering of iron ion / ferric iron binding / ferrous iron binding / iron ion transport / cytoplasm Similarity search - Function | ||||||
Biological species | Lithobates catesbeiana (American bullfrog) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.63 Å | ||||||
Authors | Jagdev, M.K. / Vasudevan, D. | ||||||
Citation | Journal: Biochim. Biophys. Acta / Year: 2017 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5xhn.cif.gz | 61.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xhn.ent.gz | 45.3 KB | Display | PDB format |
PDBx/mmJSON format | 5xhn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xh/5xhn ftp://data.pdbj.org/pub/pdb/validation_reports/xh/5xhn | HTTPS FTP |
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-Related structure data
Related structure data | 5xhiC 5xhmC 5xhoC 3ka3S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-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: Escherichia coli BL21(DE3)pLysS (bacteria) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P07798, ferroxidase | ||||
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#2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-CL / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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