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Yorodumi- PDB-4ism: Crystal structure of ferritin from Pseudo-nitzschia multiseries s... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ism | ||||||
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Title | Crystal structure of ferritin from Pseudo-nitzschia multiseries soaked with zinc | ||||||
Components | Ferritin | ||||||
Keywords | TRANSPORT PROTEIN / ferritin | ||||||
Function / homology | Function and homology information ferroxidase / ferroxidase activity / ferric iron binding / iron ion transport / intracellular iron ion homeostasis / identical protein binding Similarity search - Function | ||||||
Biological species | Pseudo-nitzschia multiseries (Diatom) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å | ||||||
Authors | Pfaffen, S. / Murphy, M.E.P. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2013 Title: Mechanism of ferrous iron binding and oxidation by ferritin from a pennate diatom. Authors: Pfaffen, S. / Abdulqadir, R. / Le Brun, N.E. / Murphy, M.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ism.cif.gz | 283.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ism.ent.gz | 241.5 KB | Display | PDB format |
PDBx/mmJSON format | 4ism.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/is/4ism ftp://data.pdbj.org/pub/pdb/validation_reports/is/4ism | HTTPS FTP |
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-Related structure data
Related structure data | 4ispC 4ittC 4itwC 4iwjC 4iwkC 4ixkC 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: 18866.980 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudo-nitzschia multiseries (Diatom) / Gene: FTN / Production host: Escherichia coli (E. coli) / References: UniProt: B6DMH6 #2: Chemical | ChemComp-ZN / #3: 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: 2.96 Å3/Da / Density % sol: 58.51 % |
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-Data collection
Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Detector | Type: ADSC QUANTUM 315r / Detector: CCD | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2→50 Å / Num. obs: 120229 / % possible obs: 99.9 % / Redundancy: 14.7 % / Rmerge(I) obs: 0.086 / Χ2: 1.1 / Net I/σ(I): 14.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→42.51 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.935 / WRfactor Rfree: 0.2427 / WRfactor Rwork: 0.1955 / Occupancy max: 1 / Occupancy min: 0.33 / FOM work R set: 0.8286 / SU B: 3.394 / SU ML: 0.096 / SU R Cruickshank DPI: 0.1562 / SU Rfree: 0.1516 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.156 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
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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: 98.81 Å2 / Biso mean: 30.0452 Å2 / Biso min: 11.98 Å2
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Refinement step | Cycle: LAST / Resolution: 2→42.51 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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