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Yorodumi- PDB-4dyz: Crystal Structure of the apo form of Human H-Ferritin variant MIC1 -
+Open data
-Basic information
Entry | Database: PDB / ID: 4dyz | ||||||
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Title | Crystal Structure of the apo form of Human H-Ferritin variant MIC1 | ||||||
Components | Ferritin heavy chain | ||||||
Keywords | OXIDOREDUCTASE / four-helix bundle | ||||||
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 / molecular replacement / Resolution: 2.3 Å | ||||||
Authors | Tezcan, F.A. / Huard, D.J.E. | ||||||
Citation | Journal: Nat.Chem.Biol. / Year: 2013 Title: Re-engineering protein interfaces yields copper-inducible ferritin cage assembly. Authors: Huard, D.J. / Kane, K.M. / Tezcan, F.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4dyz.cif.gz | 53.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4dyz.ent.gz | 38.6 KB | Display | PDB format |
PDBx/mmJSON format | 4dyz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dy/4dyz ftp://data.pdbj.org/pub/pdb/validation_reports/dy/4dyz | HTTPS FTP |
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-Related structure data
Related structure data | 4dyxC 4dyyC 4dz0C 2ceiS 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: 20047.225 Da / Num. of mol.: 1 / Mutation: L56H, R63H, E67H, K86Q, C90E, C102A, C130A 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-CU / | ||
#3: Chemical | ChemComp-CA / #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: 3.08 Å3/Da / Density % sol: 60.12 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 50 mM Tris, 10 mM calcium chloride, 4% PEG 400, soaked in 20 mM EDTA, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.98 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 17, 2011 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Rh coated flat mirror, toroidal focusing mirror Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.3→104.538 Å / Num. all: 11848 / Num. obs: 11848 / % possible obs: 100 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 42 % / Rsym value: 0.097 / Net I/σ(I): 36.1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2CEI Resolution: 2.3→90.54 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.857 / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.817 / SU B: 6.376 / SU ML: 0.158 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.292 / ESU R Free: 0.239 / 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 53.45 Å2 / Biso mean: 25.9923 Å2 / Biso min: 12.93 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→90.54 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.36 Å / Total num. of bins used: 20
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