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- PDB-8wpv: Truncated mutant (1-171) of ferritin from Ureaplasma diversum soa... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8wpv | ||||||
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Title | Truncated mutant (1-171) of ferritin from Ureaplasma diversum soaked in Fe2+ solution for 30min | ||||||
![]() | Truncated mutant of ferritin | ||||||
![]() | METAL BINDING PROTEIN / Ferritin / Iron / Fe-O cluster / 4-fold channel cavity | ||||||
Function / homology | : ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wang, W.M. / Xi, H.F. / Gong, W.J. / Ma, D.Y. / Wang, H.F. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Growth Process of Fe-O Nanoclusters with Different Sizes Biosynthesized by Protein Nanocages. Authors: Wenming Wang / Hongfang Xi / Dan Fu / Danyang Ma / Wenjun Gong / Yaqin Zhao / Xiaomei Li / Lijie Wu / Yu Guo / Guanghua Zhao / Hongfei Wang / ![]() Abstract: All protein-directed syntheses of metal nanoclusters (NCs) and nanoparticles (NPs) have attracted considerable attention because protein scaffolds provide a unique metal coordination environment and ...All protein-directed syntheses of metal nanoclusters (NCs) and nanoparticles (NPs) have attracted considerable attention because protein scaffolds provide a unique metal coordination environment and can adjust the shape and morphology of NCs and NPs. However, the detailed formation mechanisms of NCs or NPs directed by protein templates remain unclear. In this study, by taking advantage of the ferritin nanocage as a biotemplate to monitor the growth of Fe-O NCs as a function of time, we synthesized a series of iron NCs with different sizes and shapes and subsequently solved their corresponding three-dimensional atomic-scale structures by X-ray protein crystallography and cryo-electron microscopy. The time-dependent structure analyses revealed the growth process of these Fe-O NCs with the 4-fold channel of ferritin as nucleation sites. To our knowledge, the newly biosynthesized FeOGlu represents the largest Fe-O NCs with a definite atomic structure. This study contributes to our understanding of the formation mechanism of iron NCs and provides an effective method for metal NC synthesis. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 50.8 KB | Display | ![]() |
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PDB format | ![]() | 36.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3.6 MB | Display | ![]() |
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Full document | ![]() | 3.6 MB | Display | |
Data in XML | ![]() | 9.2 KB | Display | |
Data in CIF | ![]() | 12.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8w6mC ![]() 8w6qC ![]() 8w6sC ![]() 8w6uC ![]() 8w6yC ![]() 8w73C ![]() 8w74C ![]() 8w79C ![]() 8w7bC ![]() 8w7oC ![]() 8w7qC ![]() 8w7tC ![]() 8w7uC ![]() 8w7vC ![]() 8wptC ![]() 8wquC ![]() 8wqvC ![]() 8wqxC ![]() 8wqyC ![]() 8wr0C C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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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: 20027.717 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||||||
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#2: Chemical | ChemComp-FE / #3: Chemical | ChemComp-MG / | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.06 Å3/Da / Density % sol: 59.85 % |
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Crystal grow | Temperature: 279 K / Method: vapor diffusion, hanging drop / Details: Bicine, MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Oct 6, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2.059→104.27 Å / Num. obs: 29497 / % possible obs: 100 % / Redundancy: 38.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.278 / Rpim(I) all: 0.045 / Rrim(I) all: 0.282 / Χ2: 0.95 / Net I/σ(I): 16.3 |
Reflection shell | Resolution: 2.06→2.17 Å / % possible obs: 100 % / Redundancy: 38.2 % / Num. measured all: 87898 / Num. unique obs: 2301 / CC1/2: 0.482 / Rpim(I) all: 0.998 / Χ2: 0.88 / Net I/σ(I) obs: 0.9 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.059→31.926 Å
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Refine LS restraints |
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LS refinement shell |
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