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Yorodumi- PDB-5n26: X-ray structure of human heavy chain ferritin in complex with cis... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5n26 | ||||||
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Title | X-ray structure of human heavy chain ferritin in complex with cisplatin | ||||||
Components | Ferritin heavy chain | ||||||
Keywords | OXIDOREDUCTASE / ferritin | ||||||
Function / homology | Function and homology information iron ion sequestering activity / : / autolysosome / Scavenging by Class A Receptors / Golgi Associated Vesicle Biogenesis / ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / negative regulation of fibroblast proliferation / ferric iron binding ...iron ion sequestering activity / : / autolysosome / Scavenging by Class A Receptors / 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 / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | ||||||
Authors | Ferraro, G. / Merlino, A. | ||||||
Citation | Journal: Inorg Chem / Year: 2017 Title: Cisplatin Binding Sites in Human H-Chain Ferritin. Authors: Ferraro, G. / Ciambellotti, S. / Messori, L. / Merlino, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5n26.cif.gz | 60.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5n26.ent.gz | 43.7 KB | Display | PDB format |
PDBx/mmJSON format | 5n26.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n2/5n26 ftp://data.pdbj.org/pub/pdb/validation_reports/n2/5n26 | HTTPS FTP |
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-Related structure data
Related structure data | 5n27C 4y08S 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
-Protein , 1 types, 1 molecules A
#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 BL21(DE3) (bacteria) / References: UniProt: P02794, ferroxidase |
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-Non-polymers , 5 types, 238 molecules
#2: Chemical | #3: Chemical | ChemComp-73M / | #4: Chemical | ChemComp-CL / #5: Chemical | ChemComp-MG / #6: 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: 3.03 Å3/Da / Density % sol: 59.34 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 2.0 M Magnesium chloride, 0.1 M bicine pH 9.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Sep 15, 2006 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→105.7 Å / Num. obs: 16819 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.9 % / Rmerge(I) obs: 0.143 / Rpim(I) all: 0.053 / Net I/σ(I): 17.8 |
Reflection shell | Resolution: 2.05→2.09 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.588 / Mean I/σ(I) obs: 3.7 / CC1/2: 0.837 / Rpim(I) all: 0.236 / % possible all: 91.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4Y08 Resolution: 2.05→105.69 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.937 / SU B: 3.406 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R: 0.149 / ESU R Free: 0.142 / 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: 19.358 Å2
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Refinement step | Cycle: 1 / Resolution: 2.05→105.69 Å
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Refine LS restraints |
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