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Yorodumi- PDB-5oba: Structure of a modified mouse H-chain ferritin with a lanthanide ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5oba | ||||||
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Title | Structure of a modified mouse H-chain ferritin with a lanthanide binding motif | ||||||
Components | Ferritin heavy chain | ||||||
Keywords | METAL TRANSPORT / ferritin / lanthanide | ||||||
Function / homology | Function and homology information Iron uptake and transport / Golgi Associated Vesicle Biogenesis / iron ion sequestering activity / autolysosome / ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / negative regulation of fibroblast proliferation / endocytic vesicle lumen / Neutrophil degranulation ...Iron uptake and transport / Golgi Associated Vesicle Biogenesis / iron ion sequestering activity / autolysosome / ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / negative regulation of fibroblast proliferation / endocytic vesicle lumen / Neutrophil degranulation / ferric iron binding / ferrous iron binding / iron ion transport / immune response / iron ion binding / negative regulation of cell population proliferation / mitochondrion / extracellular region / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å | ||||||
Authors | Baiocco, P. / Trabuco, M.C. | ||||||
Funding support | Italy, 1items
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Citation | Journal: PLoS ONE / Year: 2018 Title: Engineered ferritin for lanthanide binding. Authors: Calisti, L. / Trabuco, M.C. / Boffi, A. / Testi, C. / Montemiglio, L.C. / des Georges, A. / Benni, I. / Ilari, A. / Taciak, B. / Bialasek, M. / Rygiel, T. / Krol, M. / Baiocco, P. / Bonamore, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5oba.cif.gz | 807.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5oba.ent.gz | 675.8 KB | Display | PDB format |
PDBx/mmJSON format | 5oba.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ob/5oba ftp://data.pdbj.org/pub/pdb/validation_reports/ob/5oba | HTTPS FTP |
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-Related structure data
Related structure data | 5obbC 3wnwS 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 22692.334 Da / Num. of mol.: 24 / Mutation: H177G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Fth1, Fth / Production host: Escherichia coli (E. coli) / References: UniProt: P09528, ferroxidase #2: Chemical | ChemComp-FE / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.49 Å3/Da / Density % sol: 64.74 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: Ammonium sulphate, Tris-HCl |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å | ||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 11, 2016 | ||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||
Reflection twin |
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Reflection | Resolution: 2.85→48.48 Å / Num. obs: 147573 / % possible obs: 100 % / Redundancy: 6.9 % / Net I/σ(I): 17.6 | ||||||||||||||||||||
Reflection shell | Resolution: 2.85→2.9 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 2.5 / Num. unique obs: 4475 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3WNW Resolution: 2.85→48.48 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.924 / SU B: 7.586 / SU ML: 0.145 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.145 / ESU R Free: 0.05 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 109.77 Å2 / Biso mean: 58.42 Å2 / Biso min: 13.97 Å2
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Refinement step | Cycle: final / Resolution: 2.85→48.48 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.848→2.921 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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