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- PDB-2z6m: Crystal structure of Human Ferritin H8 as biotemplate for noble m... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2z6m | ||||||
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Title | Crystal structure of Human Ferritin H8 as biotemplate for noble metal nanoparticle synthesis | ||||||
![]() | Ferritin heavy chain | ||||||
![]() | OXIDOREDUCTASE / Biotemplate / Iron / Iron storage / Metal-binding / Phosphorylation | ||||||
Function / homology | ![]() 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 / Iron uptake and transport / ferrous iron binding / tertiary granule lumen / iron ion transport / intracellular iron ion homeostasis / ficolin-1-rich granule lumen / iron ion binding / immune response / negative regulation of cell population proliferation / Neutrophil degranulation / extracellular exosome / extracellular region / identical protein binding / membrane / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Di Costanzo, L. / Christianson, D.W. | ||||||
![]() | ![]() Title: Directing noble metal ion chemistry within a designed ferritin protein Authors: Butts, C.A. / Swift, J. / Kang, S.G. / Di Costanzo, L. / Christianson, D.W. / Saven, J.G. / Dmochowski, I.J. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 419.1 KB | Display | ![]() |
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PDB format | ![]() | 345.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 464.3 KB | Display | ![]() |
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Full document | ![]() | 511.7 KB | Display | |
Data in XML | ![]() | 46.3 KB | Display | |
Data in CIF | ![]() | 68.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3erzC ![]() 3es3C ![]() 2fhaS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 20361.869 Da / Num. of mol.: 12 / Fragment: residues 1-176 Mutation: H13D, E64C, C90R, C102A, H105Q, E140C, K143C, E147C Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-MPD / ( #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.86 Å3/Da / Density % sol: 56.98 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: protein solution(11.0 mg/mL H8 in unbuffered 3.0mM NaN3), 2.5mL of precipitant buffer(0.1 M sodium acetate(pH 4.6), 20%(v/v) isopropanol, 0.2M CaCl2) , VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 28, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 2.72→50 Å / Num. obs: 75646 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 8.8 |
Reflection shell | Resolution: 2.72→2.82 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 1.9 / Num. unique all: 7408 / % possible all: 98.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2FHA Resolution: 2.72→50 Å / σ(F): 0 / σ(I): 1
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Refinement step | Cycle: LAST / Resolution: 2.72→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.72→2.82 Å / Rfactor Rfree: 0.357 / Rfactor Rwork: 0.317 |