+Open data
-Basic information
Entry | Database: PDB / ID: 6ljg | ||||||
---|---|---|---|---|---|---|---|
Title | Crassostrea gigas ferritin mutant-D119G | ||||||
Components | Ferritin | ||||||
Keywords | METAL BINDING PROTEIN / Crassostrea gigas / ferritin / mutant / 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: 1.799 Å | ||||||
Authors | Li, H. / Zang, J. / Tan, X. / Wang, Z. / Du, M. | ||||||
Funding support | China, 1items
| ||||||
Citation | Journal: To Be Published Title: Crassostrea gigas ferritin mutant-D119G Authors: Li, H. / Zang, J. / Tan, X. / Wang, Z. / Du, M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6ljg.cif.gz | 55.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6ljg.ent.gz | 39 KB | Display | PDB format |
PDBx/mmJSON format | 6ljg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lj/6ljg ftp://data.pdbj.org/pub/pdb/validation_reports/lj/6ljg | HTTPS FTP |
---|
-Related structure data
Related structure data | 1fhaS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| x 24|||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 19868.078 Da / Num. of mol.: 1 / Mutation: D119G 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 | ChemComp-FE / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.62 Å3/Da / Density % sol: 66.02 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion / Details: PEG 8000, CAPS/Sodium hydroxide, Sodium chloride |
-Data collection
Diffraction | Mean temperature: 93 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9785 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 9, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9785 Å / Relative weight: 1 |
Reflection | Resolution: 1.799→26.72 Å / Num. obs: 27659 / % possible obs: 99.93 % / Redundancy: 38.8 % / CC1/2: 1 / Net I/σ(I): 311 |
Reflection shell | Resolution: 1.799→1.864 Å / Num. unique obs: 2700 / CC1/2: 1 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1FHA Resolution: 1.799→26.717 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 23.21
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 60.74 Å2 / Biso mean: 29.2704 Å2 / Biso min: 16.44 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.799→26.717 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %
|