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Yorodumi- PDB-7ryw: Crystal structure of Ferritin grown by the microbatch method in t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ryw | ||||||
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Title | Crystal structure of Ferritin grown by the microbatch method in the presence of Agarose | ||||||
Components | Ferritin light chain | ||||||
Keywords | METAL BINDING PROTEIN / ferritin / crystallization / agarose / metal ions | ||||||
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: 2.09 Å | ||||||
Authors | Aditya, S. / Priyadharshine, R. / Maham, I. / Miller, D.J. / Stojanoff, V. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: Crystal structure of Ferritin grown by microbatch method in the presence of agarose Authors: Aditya, S. / Priyadharshine, R. / Maham, I. / Miller, D.J. / Stojanoff, V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ryw.cif.gz | 51.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ryw.ent.gz | 36.4 KB | Display | PDB format |
PDBx/mmJSON format | 7ryw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ry/7ryw ftp://data.pdbj.org/pub/pdb/validation_reports/ry/7ryw | HTTPS FTP |
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-Related structure data
Related structure data | 2w0oS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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 / Fragment: residues 3-172 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Equus caballus (horse) / Gene: FTL / Production host: Escherichia phage EcSzw-2 (virus) / References: UniProt: P02791 | ||||||
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#2: Chemical | ChemComp-CD / #3: Chemical | ChemComp-SO4 / | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.13 Å3/Da / Density % sol: 60.76 % |
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Crystal grow | Temperature: 290 K / Method: microbatch / Details: CdSO4, NH4SO4, Tris pH 7.4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.979 Å |
Detector | Type: ADSC HF-4M / Detector: PIXEL / Date: Aug 2, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.09→28.7 Å / Num. obs: 15632 / % possible obs: 99.8 % / Redundancy: 20 % / Biso Wilson estimate: 28.34 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.112 / Net I/σ(I): 0.935 |
Reflection shell | Resolution: 2.09→2.15 Å / Num. unique obs: 1090 / CC1/2: 0.954 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2W0O Resolution: 2.09→28.7 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 18.94 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 126.38 Å2 / Biso mean: 30.9457 Å2 / Biso min: 16.77 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.09→28.7 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6 / % reflection obs: 100 %
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