+Open data
-Basic information
Entry | Database: PDB / ID: 2z5r | ||||||
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Title | Apo-Fr with high content of Pd ions | ||||||
Components | Ferritin light chain | ||||||
Keywords | METAL BINDING PROTEIN / IRON STORAGE / LIGHT CHAIN APOFERRITIN | ||||||
Function / homology | Function and homology information ferritin complex / autolysosome / intracellular sequestering of iron ion / autophagosome / ferric iron binding / ferrous iron binding / iron ion transport / cytoplasmic vesicle / iron ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Equus caballus (horse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Ueno, T. / Hirata, K. / Abe, M. / Suzuki, M. / Abe, S. / Shimizu, N. / Yamamoto, M. / Takata, M. / Watanabe, Y. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2009 Title: Process of accumulation of metal ions on the interior surface of apo-ferritin: crystal structures of a series of apo-ferritins containing variable quantities of Pd(II) ions. Authors: Ueno, T. / Abe, M. / Hirata, K. / Abe, S. / Suzuki, M. / Shimizu, N. / Yamamoto, M. / Takata, M. / Watanabe, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2z5r.cif.gz | 51.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2z5r.ent.gz | 37.8 KB | Display | PDB format |
PDBx/mmJSON format | 2z5r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2z5r_validation.pdf.gz | 428.3 KB | Display | wwPDB validaton report |
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Full document | 2z5r_full_validation.pdf.gz | 432 KB | Display | |
Data in XML | 2z5r_validation.xml.gz | 9.7 KB | Display | |
Data in CIF | 2z5r_validation.cif.gz | 12.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z5/2z5r ftp://data.pdbj.org/pub/pdb/validation_reports/z5/2z5r | HTTPS FTP |
-Related structure data
Related structure data | 2z5pC 2z5qC 3fi6C 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
#1: Protein | Mass: 19872.428 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Equus caballus (horse) / Tissue: Spleen / Gene: FTL / Plasmid: pMK2 / Production host: Escherichia coli (E. coli) / Strain (production host): Nova Blue / References: UniProt: P02791 | ||||
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#2: Chemical | ChemComp-PD / #3: Chemical | #4: 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: 3.14 Å3/Da / Density % sol: 60.81 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: Ammonium sulfate, Cadmium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation | Monochromator: Si 111 Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.5→50 Å / Num. obs: 9397 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 11.6 % / Biso Wilson estimate: 39.084 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 33.9 | |||||||||||||||
Reflection shell | Resolution: 2.5→2.69 Å / Redundancy: 11.8 % / Rmerge(I) obs: 0.302 / Mean I/σ(I) obs: 7.2 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1DAT Resolution: 2.5→45.41 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.833 / SU B: 7.759 / SU ML: 0.18 / Cross valid method: THROUGHOUT / ESU R: 0.376 / ESU R Free: 0.292 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: THE AUTHORS USED ONLY ONE CRYSTAL FOR TWO DATA COLLECTIONS. DIFFRACTION DATA WERE COLLECTED WITH TWO DIFFERENCE WAVELENGTHS USING ONE CRYSTAL.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.593 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→45.41 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.498→2.563 Å / Total num. of bins used: 20
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