+Open data
-Basic information
Entry | Database: PDB / ID: 7vio | ||||||
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Title | Crystal structure of recombinant horse spleen apo-R168H/L169C-Fr | ||||||
Components | Ferritin light chain | ||||||
Keywords | METAL BINDING PROTEIN / ferritin | ||||||
Function / homology | Function and homology information : / intracellular sequestering of iron ion / ferric iron binding / ferrous iron binding / iron ion transport / iron ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Equus caballus (horse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Lu, C. / Peng, X. / Maity, B. / Ito, N. / Abe, S. / Wu, J. / Ueno, T. / Lu, D. | ||||||
Funding support | China, 1items
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Citation | Journal: Commun Chem / Year: 2022 Title: Design of a gold clustering site in an engineered apo-ferritin cage. Authors: Lu, C. / Maity, B. / Peng, X. / Ito, N. / Abe, S. / Sheng, X. / Ueno, T. / Lu, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7vio.cif.gz | 58.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7vio.ent.gz | 40.3 KB | Display | PDB format |
PDBx/mmJSON format | 7vio.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vi/7vio ftp://data.pdbj.org/pub/pdb/validation_reports/vi/7vio | HTTPS FTP |
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-Related structure data
Related structure data | 7vipC 7viqC 7virC 7visC 7vitC 7viuC 1datS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 19843.365 Da / Num. of mol.: 1 / Mutation: R168H/L169C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Equus caballus (horse) / Gene: FTL / Production host: Escherichia coli (E. coli) / References: UniProt: P02791 | ||||||
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#2: Chemical | ChemComp-GOL / | ||||||
#3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.2 Å3/Da / Density % sol: 61.52 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: Ammonium Sulfate, Cadmium Sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 7, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→37.31 Å / Num. obs: 42065 / % possible obs: 99.7 % / Redundancy: 1.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.028 / Rpim(I) all: 0.028 / Rrim(I) all: 0.039 / Net I/σ(I): 22.7 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.039 / Num. unique obs: 2066 / CC1/2: 0.995 / Rpim(I) all: 0.039 / Rrim(I) all: 0.055 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1dat Resolution: 1.5→37.31 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.949 / WRfactor Rfree: 0.226 / WRfactor Rwork: 0.205 / SU B: 0.779 / SU ML: 0.03 / Average fsc free: 0.9587 / Average fsc work: 0.963 / Cross valid method: FREE R-VALUE / ESU R: 0.059 / ESU R Free: 0.059 / Details: Hydrogens have not been used
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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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.462 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→37.31 Å
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Refine LS restraints |
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LS refinement shell |
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