+Open data
-Basic information
Entry | Database: PDB / ID: 5czu | ||||||
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Title | Crystal structure of FeCat-Fn | ||||||
Components | Ferritin light chain | ||||||
Keywords | METAL BINDING PROTEIN / IRON STORAGE | ||||||
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: 1.6 Å | ||||||
Authors | Abe, S. / Nakajima, H. / Kondo, M. / Nakane, T. / Nakao, T. / Ueno, T. / Watanabe, Y. | ||||||
Citation | Journal: Chem.Commun.(Camb.) / Year: 2015 Title: Construction of an enterobactin analogue with symmetrically arranged monomer subunits of ferritin Authors: Nakajima, H. / Kondo, M. / Nakane, T. / Abe, S. / Nakao, T. / Watanabe, Y. / Ueno, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5czu.cif.gz | 57.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5czu.ent.gz | 41.8 KB | Display | PDB format |
PDBx/mmJSON format | 5czu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cz/5czu ftp://data.pdbj.org/pub/pdb/validation_reports/cz/5czu | HTTPS FTP |
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-Related structure data
Related structure data | 5axsC 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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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: 19872.430 Da / Num. of mol.: 1 / Mutation: A119C, C126A 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, 181 molecules
#2: Chemical | ChemComp-4LF / | ||||||
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#3: Chemical | ChemComp-SO4 / | ||||||
#4: Chemical | ChemComp-CD / #5: Chemical | ChemComp-FE / | #6: Chemical | ChemComp-GOL / | #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: 3.1 Å3/Da / Density % sol: 60.39 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: ammonium sulfate, cadmium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 12, 2015 |
Radiation | Monochromator: Fixed exit Si (111) double crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→60 Å / Num. obs: 34034 / % possible obs: 99.9 % / Redundancy: 10.5 % / Net I/σ(I): 58 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 6.1 / % possible all: 100 |
-Processing
Software | Name: REFMAC / Version: 5.6.0117 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1DAT Resolution: 1.6→36.96 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.935 / SU B: 1.075 / SU ML: 0.039 / Cross valid method: THROUGHOUT / ESU R: 0.072 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 17.313 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→36.96 Å
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