[English] 日本語
Yorodumi- PDB-2mgh: HIGH RESOLUTION CRYSTAL STRUCTURES OF FIVE DISTAL HISTIDINE MUTAN... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2mgh | ||||||
---|---|---|---|---|---|---|---|
Title | HIGH RESOLUTION CRYSTAL STRUCTURES OF FIVE DISTAL HISTIDINE MUTANTS OF SPERM WHALE MYOGLOBIN | ||||||
Components | MYOGLOBIN | ||||||
Keywords | OXYGEN STORAGE | ||||||
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 / oxygen carrier activity / oxygen binding / peroxidase activity / heme binding / extracellular exosome / metal ion binding Similarity search - Function | ||||||
Biological species | Physeter catodon (sperm whale) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2 Å | ||||||
Authors | Arduini, R.M. / Quillin, M.L. / Phillips Jr., G.N. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1993 Title: High-resolution crystal structures of distal histidine mutants of sperm whale myoglobin. Authors: Quillin, M.L. / Arduini, R.M. / Olson, J.S. / Phillips Jr., G.N. #1: Journal: Proteins / Year: 1990 Title: Crystal Structure of Myoglobin from a Synthetic Gene Authors: Phillips Jr., G.N. / Arduini, R.M. / Springer, B.A. / Sligar, S.G. #2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1987 Title: High-Level Expression of Sperm Whale Myoglobin in Escherichia Coli Authors: Springer, B.A. / Sligar, S.G. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2mgh.cif.gz | 46.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2mgh.ent.gz | 32.8 KB | Display | PDB format |
PDBx/mmJSON format | 2mgh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2mgh_validation.pdf.gz | 816 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2mgh_full_validation.pdf.gz | 821.2 KB | Display | |
Data in XML | 2mgh_validation.xml.gz | 11.6 KB | Display | |
Data in CIF | 2mgh_validation.cif.gz | 15.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mg/2mgh ftp://data.pdbj.org/pub/pdb/validation_reports/mg/2mgh | HTTPS FTP |
-Related structure data
Related structure data | 1mobC 1mocC 1modC 2mgaC 2mgbC 2mgcC 2mgdC 2mgeC 2mgfC 2mggC 2mgiC 2mgjC 2mgkC 2mglC 2mgmC C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Atom site foot note | 1: THIS OXYGEN IS A WATER MOLECULE COORDINATED TO FE IN THE HEM GROUP. |
-Components
#1: Protein | Mass: 17355.145 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Physeter catodon (sperm whale) / Gene: SYNTHETIC GENE / References: UniProt: P02185 |
---|---|
#2: Chemical | ChemComp-SO4 / |
#3: Chemical | ChemComp-HEM / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 3.17 Å3/Da / Density % sol: 61.23 % | |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | *PLUS pH: 9 / Method: batch method / Details: micro seeding | |||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Reflection | *PLUS Highest resolution: 2 Å / % possible obs: 92.6 % / Rmerge(I) obs: 0.077 |
---|
-Processing
Software | Name: PROFFT / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2→5 Å /
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→5 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: PROFFT / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.171 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |