[English] 日本語
Yorodumi- PDB-6a4u: The first crystal structure of crustacean ferritin that is a hybr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6a4u | ||||||
---|---|---|---|---|---|---|---|
Title | The first crystal structure of crustacean ferritin that is a hybrid type of H and L ferritin | ||||||
Components | Ferritin | ||||||
Keywords | METAL BINDING PROTEIN / ferritin / crustacean / iron / ferroxidase site / nucleation site | ||||||
Function / homology | Function and homology information ferroxidase / ferroxidase activity / ferric iron binding / iron ion transport / intracellular iron ion homeostasis Similarity search - Function | ||||||
Biological species | Marsupenaeus japonicus (crustacean) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.16 Å | ||||||
Authors | Masuda, T. / Mikami, B. / Zang, J. / Zhao, G. | ||||||
Funding support | Japan, 1items
| ||||||
Citation | Journal: Protein Sci. / Year: 2018 Title: The first crystal structure of crustacean ferritin that is a hybrid type of H and L ferritin Authors: Masuda, T. / Zang, J. / Zhao, G. / Mikami, B. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6a4u.cif.gz | 508.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6a4u.ent.gz | 421.9 KB | Display | PDB format |
PDBx/mmJSON format | 6a4u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a4/6a4u ftp://data.pdbj.org/pub/pdb/validation_reports/a4/6a4u | HTTPS FTP |
---|
-Related structure data
Related structure data | 3ajoS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||||||||
Unit cell |
| |||||||||||||||
Components on special symmetry positions |
|
-Components
-Protein , 1 types, 6 molecules ABCDEF
#1: Protein | Mass: 19388.699 Da / Num. of mol.: 6 / Fragment: UNP residues 2-170 / Mutation: Q89R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Marsupenaeus japonicus (crustacean) / Plasmid: pET21d / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: T2B7E1, ferroxidase |
---|
-Non-polymers , 5 types, 1070 molecules
#2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-CL / | #5: Chemical | ChemComp-MG / #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.94 Å3/Da / Density % sol: 58.21 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 35% MPD, 100mM imidazole-HCl pH 8.0 and 200mM MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.8 Å |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Jul 18, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 |
Reflection | Resolution: 1.16→50 Å / Num. obs: 456412 / % possible obs: 98.8 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.036 / Net I/σ(I): 26.9 |
Reflection shell | Resolution: 1.16→1.18 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.464 / Num. unique obs: 22818 / Rpim(I) all: 0.327 / % possible all: 99 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3ajo Resolution: 1.16→23.59 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 14.35
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.16→23.59 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|