[English] 日本語
Yorodumi- PDB-8i8q: Crystal structure of horse spleen L-ferritin H114A mutant at -180... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8i8q | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of horse spleen L-ferritin H114A mutant at -180deg Celsius. | ||||||
Components | Ferritin light chain | ||||||
Keywords | METAL BINDING PROTEIN / Ferritin / H114A mutant / X-ray structure | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Maity, B. / Tian, J. / Abe, S. / Ueno, T. | ||||||
Funding support | Japan, 1items
| ||||||
Citation | Journal: Cryst.Growth Des. / Year: 2023 Title: Atomic-level insights into a unique semi-clathrate hydrate formed in a confined environment of porous protein crystal. Authors: Maity, B. / Tian, J. / Furuta, T. / Abe, S. / Ueno, T. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8i8q.cif.gz | 62.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8i8q.ent.gz | 43.2 KB | Display | PDB format |
PDBx/mmJSON format | 8i8q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i8/8i8q ftp://data.pdbj.org/pub/pdb/validation_reports/i8/8i8q | HTTPS FTP |
---|
-Related structure data
Related structure data | 8i6lC 8i77C 8i81C 8i8uC C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| x 24|||||||||||||||
Unit cell |
| |||||||||||||||
Components on special symmetry positions |
|
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 19805.357 Da / Num. of mol.: 1 / Mutation: H114A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Equus caballus (horse) / Gene: FTL / Plasmid: PMK2 / Production host: Escherichia coli (E. coli) / References: UniProt: P02791 |
---|
-Non-polymers , 5 types, 271 molecules
#2: Chemical | ChemComp-CD / #3: Chemical | #4: Chemical | ChemComp-CL / | #5: Chemical | #6: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | N |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.18 Å3/Da / Density % sol: 61.35 % |
---|---|
Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8 Details: Ammonium sulfate (0.5-1.0M), Cadmium sulfate(12-20mM) Temp details: Non-shaking incubation |
-Data collection
Diffraction | Mean temperature: 93.15 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E DW / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Aug 2, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→19.109 Å / Num. obs: 41908 / % possible obs: 100 % / Redundancy: 8.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.064 / Rrim(I) all: 0.068 / Net I/σ(I): 25 |
Reflection shell | Resolution: 1.5→1.53 Å / Rmerge(I) obs: 0.438 / Num. unique obs: 2024 / CC1/2: 0.918 / Rrim(I) all: 0.478 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→19.1 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.955 / SU B: 0.903 / SU ML: 0.034 / Cross valid method: FREE R-VALUE / ESU R: 0.056 / ESU R Free: 0.056 Details: Hydrogens have been added in their riding positions
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 10.184 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→19.1 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|