+Open data
-Basic information
Entry | Database: PDB / ID: 7dlb | ||||||
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Title | Crassostrea gigas ferritin mutant-D119K | ||||||
Components | Ferritin | ||||||
Keywords | METAL BINDING PROTEIN / Crassostrea gigas / Ferritin / Iron | ||||||
Function / homology | Function and homology information ferroxidase / ferroxidase activity / ferric iron binding / iron ion transport / intracellular iron ion homeostasis Similarity search - Function | ||||||
Biological species | Crassostrea gigas (Pacific oyster) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.502 Å | ||||||
Authors | Li, H. / Zang, J. / Wang, Z. / Du, M. | ||||||
Funding support | China, 1items
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Citation | Journal: To Be Published Title: Crassostrea gigas ferritin mutant-D119K Authors: Li, H. / Zang, J. / 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 | 7dlb.cif.gz | 83.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7dlb.ent.gz | 62.8 KB | Display | PDB format |
PDBx/mmJSON format | 7dlb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dl/7dlb ftp://data.pdbj.org/pub/pdb/validation_reports/dl/7dlb | 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 20011.283 Da / Num. of mol.: 2 / Mutation: D119K 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 #2: Chemical | #3: Water | ChemComp-HOH / | 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: 3.56 Å3/Da / Density % sol: 65.48 % |
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Crystal grow | Temperature: 293 K / Method: evaporation / Details: MPD, Tris base/ Hydrochloric acid, Sodium chloride |
-Data collection
Diffraction | Mean temperature: 90 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9375 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 12, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9375 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→29.555 Å / Num. obs: 19777 / % possible obs: 100 % / Redundancy: 9.5 % / CC1/2: 1 / Net I/σ(I): 5.1 |
Reflection shell | Resolution: 2.5→2.592 Å / Num. unique obs: 1972 / CC1/2: 1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1FHA Resolution: 2.502→29.555 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 26.65 / 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: 75.2 Å2 / Biso mean: 41.4874 Å2 / Biso min: 27.84 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.502→29.555 Å
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