+Open data
-Basic information
Entry | Database: PDB / ID: 1j52 | ||||||
---|---|---|---|---|---|---|---|
Title | Recombinant sperm whale myoglobin in the presence of 7atm xenon | ||||||
Components | myoglobin | ||||||
Keywords | OXYGEN STORAGE/TRANSPORT / oxygen transport / heme / muscle protein / xenon / internal cavities / OXYGEN STORAGE-TRANSPORT COMPLEX | ||||||
Function / homology | Function and homology information nitrite reductase activity / Oxidoreductases; Acting on other nitrogenous compounds as donors / sarcoplasm / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / removal of superoxide radicals / peroxidase activity / oxygen carrier activity / oxygen binding / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | Physeter catodon (sperm whale) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Liong, E.C. / Phillips Jr., G.N. | ||||||
Citation | Journal: To be Published Title: Internal Cavities in Myoglobin: Implications for Protein Action Authors: Radding, W. / Liong, E.C. / Phillips Jr., G.N. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1j52.cif.gz | 48.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1j52.ent.gz | 33.3 KB | Display | PDB format |
PDBx/mmJSON format | 1j52.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j5/1j52 ftp://data.pdbj.org/pub/pdb/validation_reports/j5/1j52 | HTTPS FTP |
---|
-Related structure data
Related structure data | 1mbw S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 17365.164 Da / Num. of mol.: 1 / Mutation: D122N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Physeter catodon (sperm whale) / Production host: Escherichia coli (E. coli) / References: UniProt: P02185 | ||
---|---|---|---|
#2: Chemical | ChemComp-SO4 / | ||
#3: Chemical | ChemComp-HEM / | ||
#4: Chemical | ChemComp-XE / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 3.2 Å3/Da / Density % sol: 61.61 % |
---|---|
Crystal grow | pH: 9 / Details: 2.6-3.0 M (NH4)2SO4, 20 mM TRIS, 1 mM EDTA, PH 9.0 |
-Data collection
Diffraction | Mean temperature: 295 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Apr 24, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 16336 / % possible obs: 93.1 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.067 |
-Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1MBW 1mbw Resolution: 1.9→5 Å / Cross valid method: FREE R / σ(F): 0
| ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→5 Å
| ||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||
Xplor file |
|