[English] 日本語
Yorodumi- PDB-7bom: Crystal structure of recombinant horse spleen apo-R52C/E56C/R59C/... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7bom | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of recombinant horse spleen apo-R52C/E56C/R59C/E63C-Fr immobilized with gold ions. | ||||||
Components | Ferritin light chain | ||||||
Keywords | METAL BINDING PROTEIN / IRON STORAGE | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å | ||||||
Authors | Hishikawa, Y. / Maity, B. / Ito, N. / Abe, S. / Lu, D. / Ueno, T. | ||||||
Funding support | Japan, 1items
| ||||||
Citation | Journal: Chem Lett. / Year: 2021 Title: Design of Multinuclear Gold Binding Site at the Two-fold Symmetric Interface of the Ferritin Cage Authors: Hishikawa, Y. / Maity, B. / Ito, N. / Abe, S. / Lu, D. / Ueno, T. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7bom.cif.gz | 56.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7bom.ent.gz | 40.4 KB | Display | PDB format |
PDBx/mmJSON format | 7bom.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bo/7bom ftp://data.pdbj.org/pub/pdb/validation_reports/bo/7bom | HTTPS FTP |
---|
-Related structure data
Related structure data | 7bonC 1datS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| x 24||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-Components
-Protein , 1 types, 1 molecules X
#1: Protein | Mass: 19712.383 Da / Num. of mol.: 1 / Mutation: R53C,E57C,R60C,E64C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Equus caballus (horse) / Gene: FTL / Production host: Escherichia coli (E. coli) / References: UniProt: P02791 |
---|
-Non-polymers , 7 types, 153 molecules
#2: Chemical | ChemComp-AU / #3: Chemical | ChemComp-CD / #4: Chemical | ChemComp-SO4 / | #5: Chemical | ChemComp-EDO / | #6: Chemical | ChemComp-CL / | #7: Chemical | ChemComp-NA / | #8: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.28 Å3/Da / Density % sol: 62.53 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: Ammonium sulphate, Cadmium sulphate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1.03556 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 10, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03556 Å / Relative weight: 1 |
Reflection | Resolution: 1.93→30.73 Å / Num. obs: 19871 / % possible obs: 99.85 % / Redundancy: 11.6 % / CC1/2: 0.98 / Rpim(I) all: 0.018 / Rrim(I) all: 0.061 / Net I/σ(I): 12.76 |
Reflection shell | Resolution: 1.93→2 Å / Num. unique obs: 1952 / CC1/2: 0.98 / CC star: 0.995 / Rpim(I) all: 0.094 / Rrim(I) all: 0.319 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1DAT Resolution: 1.93→30.73 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.196 / SU ML: 0.066 / Cross valid method: THROUGHOUT / ESU R: 0.111 / ESU R Free: 0.11
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.678 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.93→30.73 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|