+Open data
-Basic information
Entry | Database: PDB / ID: 3wvw | ||||||
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Title | Crystal structure of RuCO/apo-WTFr | ||||||
Components | Ferritin light chain | ||||||
Keywords | METAL BINDING PROTEIN / IRON STORAGE | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Fujita, K. / Tanaka, Y. / Abe, S. / Hikage, T. / Kuchimaru, T. / Kizaka-Kondoh, S. / Ueno, T. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2014 Title: Intracellular CO release from composite of ferritin and ruthenium carbonyl complexes. Authors: Fujita, K. / Tanaka, Y. / Sho, T. / Ozeki, S. / Abe, S. / Hikage, T. / Kuchimaru, T. / Kizaka-Kondoh, 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 | 3wvw.cif.gz | 54.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3wvw.ent.gz | 40.4 KB | Display | PDB format |
PDBx/mmJSON format | 3wvw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3wvw_validation.pdf.gz | 459.9 KB | Display | wwPDB validaton report |
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Full document | 3wvw_full_validation.pdf.gz | 460.5 KB | Display | |
Data in XML | 3wvw_validation.xml.gz | 10.7 KB | Display | |
Data in CIF | 3wvw_validation.cif.gz | 14.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wv/3wvw ftp://data.pdbj.org/pub/pdb/validation_reports/wv/3wvw | HTTPS FTP |
-Related structure data
Related structure data | 3wvuC 3wvvC 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 A
#1: Protein | Mass: 19872.428 Da / Num. of mol.: 1 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, 151 molecules
#2: Chemical | #3: Chemical | ChemComp-SO4 / | #4: Chemical | ChemComp-EDO / #5: Chemical | #6: Chemical | ChemComp-RU1 / | #7: 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: 60.99 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 1M ammonium sulfate, 20 mM cadmium sulfate, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Feb 17, 2014 |
Radiation | Monochromator: CONFOCAL MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 17978 / % possible obs: 99.9 % / Redundancy: 20.5 % / Biso Wilson estimate: 16.16 Å2 / Net I/σ(I): 44.51 |
Reflection shell | Resolution: 2→2.07 Å / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1DAT Resolution: 2→21.43 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.94 / SU B: 2.504 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.124 / ESU R Free: 0.124 / 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 mean: 20.7 Å2
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Refinement step | Cycle: LAST / Resolution: 2→21.43 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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