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Yorodumi- PDB-7rzx: Crystal Structure of Ferritin grown by microbatch method in prese... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7rzx | ||||||
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Title | Crystal Structure of Ferritin grown by microbatch method in presence of agarose and electric field 4.3KV | ||||||
Components | Ferritin light chain | ||||||
Keywords | METAL BINDING PROTEIN / ferritin / crystallization / agarose / electric field / 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: 2.44 Å | ||||||
Authors | Aditya, S. / Priyadharshine, R. / Maham, I. / Miller, J.D. / 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 presence of agarose and electric field 4.3KV Authors: Aditya, S. / Priyadharshine, R. / Maham, I. / Miller, J.D. / Stojanoff, V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7rzx.cif.gz | 51.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7rzx.ent.gz | 36.2 KB | Display | PDB format |
PDBx/mmJSON format | 7rzx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rz/7rzx ftp://data.pdbj.org/pub/pdb/validation_reports/rz/7rzx | 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: residue 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: 3.11 Å3/Da / Density % sol: 60.48 % |
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Crystal grow | Temperature: 290 K / Method: microbatch / Details: CdSO4,NH4SO4,Tris pH7.4 |
-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: 2.44→28.63 Å / Num. obs: 9949 / % possible obs: 99.8 % / Redundancy: 20 % / Biso Wilson estimate: 35.88 Å2 / CC1/2: 0.998 / Net I/σ(I): 0.828 |
Reflection shell | Resolution: 2.44→2.51 Å / Num. unique obs: 704 / CC1/2: 0.766 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2W0O Resolution: 2.44→28.63 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 22.83 / 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: 227.7 Å2 / Biso mean: 38.6369 Å2 / Biso min: 22.04 Å2 | ||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.44→28.63 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: 4 / % reflection obs: 100 %
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