+Open data
-Basic information
Entry | Database: PDB / ID: 7w7j | ||||||
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Title | Crystal structure of IrCp* immobilized apo-R52H-rHLFr (25 equiv) | ||||||
Components | Ferritin light chain | ||||||
Keywords | METAL TRANSPORT / Iron storage protein / Ir binding / METAL BINDING PROTEIN | ||||||
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: 1.5 Å | ||||||
Authors | Taher, M. / Maity, B. / Nakane, T. / Abe, S. / Mazumdar, S. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2022 Title: Controlled Uptake of an Iridium Complex inside Engineered apo-Ferritin Nanocages: Study of Structure and Catalysis. Authors: Taher, M. / Maity, B. / Nakane, T. / Abe, S. / Ueno, T. / Mazumdar, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7w7j.cif.gz | 61.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7w7j.ent.gz | 42.4 KB | Display | PDB format |
PDBx/mmJSON format | 7w7j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7w7j_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 7w7j_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 7w7j_validation.xml.gz | 11.9 KB | Display | |
Data in CIF | 7w7j_validation.cif.gz | 17.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w7/7w7j ftp://data.pdbj.org/pub/pdb/validation_reports/w7/7w7j | HTTPS FTP |
-Related structure data
Related structure data | 7emlC 7emmC 1datS 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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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: 19853.381 Da / Num. of mol.: 1 / Mutation: R52H 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 , 6 types, 241 molecules
#2: Chemical | ChemComp-EDO / | ||||||
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#3: Chemical | ChemComp-IR / | ||||||
#4: Chemical | ChemComp-CD / #5: Chemical | ChemComp-CL / | #6: Chemical | #7: Water | ChemComp-HOH / | |
-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: 3.19 Å3/Da / Density % sol: 61.45 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: Ammonium sulfate (0.5-1.0M), Cadmium sulfate(12-20mM) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Nov 9, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→19.086 Å / Num. obs: 41390 / % possible obs: 99.3 % / Redundancy: 4.4 % / CC1/2: 0.997 / Net I/σ(I): 12 |
Reflection shell | Resolution: 1.5→1.53 Å / Num. unique obs: 2000 / CC1/2: 0.366 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1dat Resolution: 1.5→19.086 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.951 / WRfactor Rfree: 0.167 / WRfactor Rwork: 0.145 / SU B: 1.618 / SU ML: 0.056 / Average fsc free: 0.8938 / Average fsc work: 0.8971 / Cross valid method: FREE R-VALUE / ESU R: 0.064 / ESU R Free: 0.067 Details: Hydrogens have been added in their riding positions
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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: 15.52 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→19.086 Å
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Refine LS restraints |
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LS refinement shell |
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