+Open data
-Basic information
Entry | Database: PDB / ID: 3af9 | ||||||
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Title | Crystal Structure of Pd(allyl)/apo-C48AFr | ||||||
Components | Ferritin light chain | ||||||
Keywords | METAL BINDING PROTEIN / Iron Storage Protein / Light Chain Ferritin / 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: 1.85 Å | ||||||
Authors | Abe, S. / Hikage, T. / Watanabe, Y. / Kitagawa, S. / Ueno, T. | ||||||
Citation | Journal: Inorg.Chem. / Year: 2010 Title: Mechanism of Accumulation and Incorporation of Organometallic Pd Complexes into the Protein Nanocage of apo-Ferritin. Authors: Abe, S. / Hikage, T. / 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 | 3af9.cif.gz | 55.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3af9.ent.gz | 40.2 KB | Display | PDB format |
PDBx/mmJSON format | 3af9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/af/3af9 ftp://data.pdbj.org/pub/pdb/validation_reports/af/3af9 | HTTPS FTP |
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-Related structure data
Related structure data | 3af7C 3af8C 1datS C: citing same article (ref.) S: Starting model for refinement |
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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 X
#1: Protein | Mass: 19840.363 Da / Num. of mol.: 1 / Mutation: C48A 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 , 6 types, 166 molecules
#2: Chemical | ChemComp-SO4 / | ||||||||
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#3: Chemical | #4: Chemical | ChemComp-PLL / | #5: Chemical | ChemComp-PD / | #6: Chemical | ChemComp-EDO / #7: Water | ChemComp-HOH / | |
-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: 61.41 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: ammonium sulfate, cadmium sulfate, pH 7, 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: BL41XU / Wavelength: 0.508 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Nov 26, 2009 |
Radiation | Monochromator: Rotated-inclined double-crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.508 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→30 Å / Num. obs: 22730 / % possible obs: 100 % / Redundancy: 11.3 % / Biso Wilson estimate: 16.771 Å2 / Rmerge(I) obs: 0.094 |
Reflection shell | Resolution: 1.85→1.92 Å / Redundancy: 11.6 % / Rmerge(I) obs: 0.272 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1DAT Resolution: 1.85→25.55 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.935 / SU B: 1.872 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.109 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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 mean: 16.087 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→25.55 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.852→1.899 Å / Total num. of bins used: 20
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