+Open data
-Basic information
Entry | Database: PDB / ID: 6i9p | ||||||
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Title | Iron-free state of Rana catesbeiana H' ferritin variant H54N | ||||||
Components | Ferritin, middle subunit | ||||||
Keywords | OXIDOREDUCTASE / Rana Catesbeiana H' ferritin / ferroxidase process / H54N variant / iron-free state | ||||||
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 | Lithobates catesbeiana (American bullfrog) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 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 | 6i9p.cif.gz | 104.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6i9p.ent.gz | 80.2 KB | Display | PDB format |
PDBx/mmJSON format | 6i9p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6i9p_validation.pdf.gz | 417.1 KB | Display | wwPDB validaton report |
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Full document | 6i9p_full_validation.pdf.gz | 417.5 KB | Display | |
Data in XML | 6i9p_validation.xml.gz | 13.3 KB | Display | |
Data in CIF | 6i9p_validation.cif.gz | 21.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i9/6i9p ftp://data.pdbj.org/pub/pdb/validation_reports/i9/6i9p | HTTPS FTP |
-Related structure data
Related structure data | 6i9tC 6iafC 6iajC 4lqhS S: Starting model for refinement C: citing same article (ref.) |
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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-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: 3.27 Å3/Da / Density % sol: 62.44 % |
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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: 0.8856 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: 0.8856 Å / Relative weight: 1 |
Reflection | Resolution: 1.25→21.24 Å / Num. obs: 73567 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 14.1 % / Biso Wilson estimate: 9.1 Å2 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.021 / Rrim(I) all: 0.079 / Net I/σ(I): 19.1 |
Reflection shell | Resolution: 1.25→1.32 Å / Redundancy: 13.5 % / Rmerge(I) obs: 0.418 / Mean I/σ(I) obs: 6.2 / Num. unique obs: 10565 / Rpim(I) all: 0.122 / Rrim(I) all: 0.45 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4LQH Resolution: 1.25→21.1 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.977 / SU B: 0.729 / SU ML: 0.016 / Cross valid method: THROUGHOUT / ESU R: 0.029 / ESU R Free: 0.029 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 10.724 Å2
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Refine analyze | Luzzati coordinate error obs: 0.116 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.25→21.1 Å
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Refine LS restraints |
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