+Open data
-Basic information
Entry | Database: PDB / ID: 6lij | ||||||
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Title | Crassostrea gigas ferritin | ||||||
Components | Ferritin | ||||||
Keywords | METAL BINDING PROTEIN / Crassostrea gigas / Ferritin / Iron | ||||||
Function / homology | Function and homology information ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / ferric iron binding / ferrous iron binding / iron ion transport / cytosol Similarity search - Function | ||||||
Biological species | Crassostrea gigas (Pacific oyster) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Li, H. / Zang, J. / Tan, X. / Wang, Z. / Du, M. | ||||||
Funding support | China, 1items
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Citation | Journal: To Be Published Title: Crassostrea gigas ferritin Authors: Li, H. / Zang, J. / Tan, X. / Wang, Z. / Du, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6lij.cif.gz | 50.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6lij.ent.gz | 35.6 KB | Display | PDB format |
PDBx/mmJSON format | 6lij.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/li/6lij ftp://data.pdbj.org/pub/pdb/validation_reports/li/6lij | HTTPS FTP |
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-Related structure data
Related structure data | 1fhaS S: Starting model for refinement |
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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: 19794.918 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Crassostrea gigas (Pacific oyster) / Gene: fer, CGI_10027591 / Production host: Escherichia coli (E. coli) / References: UniProt: Q70MM3, ferroxidase |
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#2: Chemical | ChemComp-MG / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.23 Å3/Da / Density % sol: 61.86 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion Details: Magnesium chloride hexahydrate, Tris(hydroxymethyl)aminomethane, 1,6-Hexanediol |
-Data collection
Diffraction | Mean temperature: 93 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 21, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9785 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→35.22 Å / Num. obs: 15887 / % possible obs: 100 % / Redundancy: 3 % / CC1/2: 0.75 / Net I/σ(I): 1.36 |
Reflection shell | Resolution: 2.1→2.175 Å / Num. unique obs: 1533 / CC1/2: 0.75 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1FHA Resolution: 2.1→35.22 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 20.4
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 57.51 Å2 / Biso mean: 22.9449 Å2 / Biso min: 15.43 Å2 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.1→35.22 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %
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