+Open data
-Basic information
Entry | Database: PDB / ID: 3o7r | ||||||
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Title | Crystal structure of Ru(p-cymene)/apo-H49AFr | ||||||
Components | Ferritin light chain | ||||||
Keywords | METAL BINDING PROTEIN / IRON STORAGE PROTEIN / LIGHT CHAIN APOFERRITIN / ARTIFICIAL METALLOPROTEIN | ||||||
Function / homology | Function and homology information intracellular ferritin complex / 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: 1.9 Å | ||||||
Authors | Takezawa, Y. / Bockmann, P. / Sugi, N. / Wang, Z. / Abe, S. / Murakami, T. / Hikage, T. / Erker, G. / Watanabe, Y. / Kitagawa, S. / Ueno, T. | ||||||
Citation | Journal: J.CHEM.SOC.,DALTON TRANS. / Year: 2011 Title: Incorporation of organometallic Ru complexes into apo-ferritin cage. Authors: Takezawa, Y. / Bockmann, P. / Sugi, N. / Wang, Z. / Abe, S. / Murakami, T. / Hikage, T. / Erker, G. / Watanabe, Y. / Kitagawa, S. / Ueno, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3o7r.cif.gz | 55.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3o7r.ent.gz | 41.7 KB | Display | PDB format |
PDBx/mmJSON format | 3o7r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o7/3o7r ftp://data.pdbj.org/pub/pdb/validation_reports/o7/3o7r | HTTPS FTP |
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-Related 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: 19789.314 Da / Num. of mol.: 1 / Mutation: H49A, L93P Source method: isolated from a genetically manipulated source Source: (gene. exp.) Equus caballus (horse) / Gene: FTL / Plasmid: PMK2 / Production host: Escherichia coli (E. coli) / Strain (production host): NOVA BLUE / References: UniProt: P02791 |
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-Non-polymers , 5 types, 195 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-EDO / #6: Water | ChemComp-HOH / | |
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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: 3.15 Å3/Da / Density % sol: 60.92 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: AMMONIUM SULFATE, CADMIUM SLFATE, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Feb 11, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→30 Å / Num. obs: 20743 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→24.28 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.929 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 2.795 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R: 0.136 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 87.67 Å2 / Biso mean: 23.164 Å2 / Biso min: 3.64 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→24.28 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
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