+Open data
-Basic information
Entry | Database: PDB / ID: 7vit | ||||||
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Title | Crystal structure of Au(400EQ)-apo-R168H/L169C-rHLFr | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Lu, C. / Peng, X. / Maity, B. / Ito, N. / Abe, S. / 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 | 7vit.cif.gz | 60.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7vit.ent.gz | 41.7 KB | Display | PDB format |
PDBx/mmJSON format | 7vit.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7vit_validation.pdf.gz | 5.7 MB | Display | wwPDB validaton report |
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Full document | 7vit_full_validation.pdf.gz | 5.7 MB | Display | |
Data in XML | 7vit_validation.xml.gz | 11.6 KB | Display | |
Data in CIF | 7vit_validation.cif.gz | 17.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vi/7vit ftp://data.pdbj.org/pub/pdb/validation_reports/vi/7vit | HTTPS FTP |
-Related structure data
Related structure data | 7vioC 7vipC 7viqC 7virC 7visC 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
-Protein , 1 types, 1 molecules A
#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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-Non-polymers , 5 types, 245 molecules
#2: Chemical | #3: Chemical | ChemComp-AU / #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 3.1 Å3/Da / Density % sol: 60.29 % |
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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: ROTATING ANODE / Type: RIGAKU FR-X / Wavelength: 1.540562 Å |
Detector | Type: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Feb 2, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.540562 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→12.957 Å / Num. obs: 20431 / % possible obs: 99.7 % / Redundancy: 10.2 % / CC1/2: 0.996 / Rmerge(I) obs: 0.142 / Rpim(I) all: 0.046 / Rrim(I) all: 0.149 / Net I/σ(I): 17.7 |
Reflection shell | Resolution: 1.9→1.94 Å / Rmerge(I) obs: 0.651 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 1364 / CC1/2: 0.874 / Rpim(I) all: 0.249 / Rrim(I) all: 0.698 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1dat Resolution: 1.9→12.957 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.935 / WRfactor Rfree: 0.225 / WRfactor Rwork: 0.187 / SU B: 2.675 / SU ML: 0.079 / Average fsc free: 0.9434 / Average fsc work: 0.9511 / Cross valid method: FREE R-VALUE / ESU R: 0.133 / ESU R Free: 0.126 Details: Hydrogens have been used if present in the input file
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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: 17.355 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→12.957 Å
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Refine LS restraints |
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LS refinement shell |
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