+Open data
-Basic information
Entry | Database: PDB / ID: 8i6l | ||||||
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Title | Crystal structure of horse spleen L-ferritin at -180deg Celsius. | ||||||
Components | Ferritin light chain | ||||||
Keywords | METAL BINDING PROTEIN / Ferritin / -180deg Celsius | ||||||
Function / homology | Function and homology information : / 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 / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Maity, B. / Tian, J. / Abe, S. / Ueno, T. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Cryst.Growth Des. / Year: 2023 Title: Atomic-level insights into a unique semi-clathrate hydrate formed in a confined environment of porous protein crystal. Authors: Maity, B. / Tian, J. / Furuta, T. / Abe, 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 | 8i6l.cif.gz | 63.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8i6l.ent.gz | 44.3 KB | Display | PDB format |
PDBx/mmJSON format | 8i6l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i6/8i6l ftp://data.pdbj.org/pub/pdb/validation_reports/i6/8i6l | HTTPS FTP |
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-Related structure data
Related structure data | 8i77C 8i81C 8i8qC 8i8uC 1datS S: Starting model for refinement C: citing same article (ref.) |
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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
-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) / References: UniProt: P02791 |
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-Non-polymers , 5 types, 277 molecules
#2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-CD / #4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-CL / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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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: 3.18 Å3/Da / Density % sol: 61.23 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 8 Details: Ammonium sulfate (0.5-1.0M), Cadmium sulfate(12-20mM) Temp details: No shaking incubation |
-Data collection
Diffraction | Mean temperature: 93.15 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E DW / Wavelength: 1.542 Å |
Detector | Type: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Jul 7, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.542 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→18.581 Å / Num. obs: 41630 / % possible obs: 99.6 % / Redundancy: 10 % / CC1/2: 1 / Rmerge(I) obs: 0.054 / Net I/σ(I): 26.8 |
Reflection shell | Resolution: 1.5→1.53 Å / Num. unique obs: 1995 / CC1/2: 0.946 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1DAT Resolution: 1.5→18.581 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.957 / SU B: 0.873 / SU ML: 0.033 / Cross valid method: FREE R-VALUE / ESU R: 0.056 / ESU R Free: 0.057 Details: Hydrogens have been added in their 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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 10.88 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→18.581 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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