+Open data
-Basic information
Entry | Database: PDB / ID: 5xhi | ||||||
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Title | Crystal structure of Frog M-ferritin D38A mutant | ||||||
Components | Ferritin, middle subunit | ||||||
Keywords | OXIDOREDUCTASE / Ferritin / M-ferritin | ||||||
Function / homology | Function and homology information 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 | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.26 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 | 5xhi.cif.gz | 107.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xhi.ent.gz | 82.7 KB | Display | PDB format |
PDBx/mmJSON format | 5xhi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5xhi_validation.pdf.gz | 434.4 KB | Display | wwPDB validaton report |
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Full document | 5xhi_full_validation.pdf.gz | 435.7 KB | Display | |
Data in XML | 5xhi_validation.xml.gz | 12.4 KB | Display | |
Data in CIF | 5xhi_validation.cif.gz | 19 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xh/5xhi ftp://data.pdbj.org/pub/pdb/validation_reports/xh/5xhi | HTTPS FTP |
-Related structure data
Related structure data | 5xhmC 5xhnC 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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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 20360.896 Da / Num. of mol.: 1 / Mutation: D38A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rana 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: 3.16 Å3/Da / Density % sol: 61.05 % / Description: Cubic |
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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: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.8266 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 30, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8266 Å / Relative weight: 1 |
Reflection | Resolution: 1.26→31.12 Å / Num. obs: 72072 / % possible obs: 100 % / Redundancy: 14.5 % / Net I/σ(I): 15.9 |
Reflection shell | Resolution: 1.26→1.28 Å / Redundancy: 14.4 % / Mean I/σ(I) obs: 5.4 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3KA3 Resolution: 1.26→31.12 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.966 / SU B: 0.862 / SU ML: 0.017 / Cross valid method: THROUGHOUT / ESU R: 0.03 / ESU R Free: 0.032 / 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: 11.99 Å2
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Refinement step | Cycle: LAST / Resolution: 1.26→31.12 Å
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Refine LS restraints |
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