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Yorodumi- PDB-6ftv: X-ray structure of human heavy chain ferritin in complex with NAMI A -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ftv | ||||||
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Title | X-ray structure of human heavy chain ferritin in complex with NAMI A | ||||||
Components | Ferritin heavy chain | ||||||
Keywords | TRANSPORT PROTEIN / metallodrug-protein / ferritin / ferroxidase activity / ruthenium / antimetastatic / anticancer agent | ||||||
Function / homology | Function and homology information iron ion sequestering activity / Scavenging by Class A Receptors / intracellular ferritin complex / autolysosome / Golgi Associated Vesicle Biogenesis / ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / negative regulation of fibroblast proliferation / ferric iron binding ...iron ion sequestering activity / Scavenging by Class A Receptors / intracellular ferritin complex / autolysosome / Golgi Associated Vesicle Biogenesis / ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / negative regulation of fibroblast proliferation / ferric iron binding / ferrous iron binding / Iron uptake and transport / tertiary granule lumen / iron ion transport / intracellular iron ion homeostasis / ficolin-1-rich granule lumen / immune response / iron ion binding / negative regulation of cell population proliferation / Neutrophil degranulation / extracellular exosome / extracellular region / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å | ||||||
Authors | Merlino, A. / Ferraro, G. | ||||||
Citation | Journal: Dalton Trans / Year: 2018 Title: The NAMI A - human ferritin system: a biophysical characterization. Authors: Ciambellotti, S. / Pratesi, A. / Severi, M. / Ferraro, G. / Alessio, E. / Merlino, A. / Messori, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ftv.cif.gz | 66.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ftv.ent.gz | 49 KB | Display | PDB format |
PDBx/mmJSON format | 6ftv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ft/6ftv ftp://data.pdbj.org/pub/pdb/validation_reports/ft/6ftv | HTTPS FTP |
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-Related structure data
Related structure data | 5n27S 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: 21124.459 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FTH1, FTH, FTHL6, OK/SW-cl.84, PIG15 / Production host: Escherichia coli (E. coli) / References: UniProt: P02794, ferroxidase | ||||||
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#2: Chemical | ChemComp-CL / #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-RU / | #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: 2.99 Å3/Da / Density % sol: 58.86 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 2.0 M MgCl2, 0.1 M bicine pH 9.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.9677 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Oct 23, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9677 Å / Relative weight: 1 |
Reflection | Resolution: 1.58→105.3 Å / Num. obs: 35972 / % possible obs: 99.7 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 14.5 |
Reflection shell | Resolution: 1.58→1.61 Å / Redundancy: 7.8 % / Mean I/σ(I) obs: 2 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5N27 Resolution: 1.58→105.3 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.39 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R: 0.062 / ESU R Free: 0.07 / 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: 25.194 Å2
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Refinement step | Cycle: 1 / Resolution: 1.58→105.3 Å
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Refine LS restraints |
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