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Yorodumi- PDB-6iaj: Sixty minutes iron loaded Rana Catesbeiana H' ferritin variant H54N -
+Open data
-Basic information
Entry | Database: PDB / ID: 6iaj | ||||||
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Title | Sixty minutes iron loaded Rana Catesbeiana H' ferritin variant H54N | ||||||
Components | Ferritin, middle subunit | ||||||
Keywords | OXIDOREDUCTASE / Rana catesbeiana H' ferritin / ferroxidase process / H54N variant / sixty minutes iron loaded / time-controlled iron loading | ||||||
Function / homology | Function and homology information ferroxidase / ferroxidase activity / ferric iron binding / iron ion transport / intracellular iron ion homeostasis Similarity search - Function | ||||||
Biological species | Lithobates catesbeiana (American bullfrog) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å | ||||||
Authors | Pozzi, C. / Di Pisa, F. / Mangani, S. | ||||||
Citation | Journal: J.Inorg.Biochem. / Year: 2019 Title: Effect of the point mutation H54N on the ferroxidase process of Rana catesbeiana H' ferritin. Authors: Pozzi, C. / Di Pisa, F. / Lalli, D. / Rosa, C. / Turano, P. / Mangani, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6iaj.cif.gz | 67.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6iaj.ent.gz | 49.1 KB | Display | PDB format |
PDBx/mmJSON format | 6iaj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ia/6iaj ftp://data.pdbj.org/pub/pdb/validation_reports/ia/6iaj | HTTPS FTP |
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-Related structure data
Related structure data | 6i9pC 6i9tC 6iafC 4lqhS 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: 20599.137 Da / Num. of mol.: 1 / Mutation: H54N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lithobates catesbeiana (American bullfrog) Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: P07798, ferroxidase | ||||||
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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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.28 Å3/Da / Density % sol: 62.57 % |
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Crystal grow | Temperature: 281 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 1.6-2.0 M MgCl2 and 0.1 M bicine pH 9.0 / PH range: 8-9 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.95372 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 8, 2012 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95372 Å / Relative weight: 1 |
Reflection | Resolution: 1.62→24.6 Å / Num. obs: 34490 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 7.8 % / Biso Wilson estimate: 7.77 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.045 / Rrim(I) all: 0.13 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 1.62→1.71 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 3.6 / Num. unique obs: 4928 / CC1/2: 0.898 / Rpim(I) all: 0.18 / Rrim(I) all: 0.463 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4LQH Resolution: 1.62→23.98 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.33 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.071 / ESU R Free: 0.074
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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: 13.401 Å2
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Refine analyze | Luzzati coordinate error obs: 0.146 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.62→23.98 Å
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Refine LS restraints |
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