[English] 日本語
Yorodumi- PDB-1mbi: X-RAY CRYSTAL STRUCTURE OF THE FERRIC SPERM WHALE MYOGLOBIN: IMID... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1mbi | ||||||
---|---|---|---|---|---|---|---|
Title | X-RAY CRYSTAL STRUCTURE OF THE FERRIC SPERM WHALE MYOGLOBIN: IMIDAZOLE COMPLEX AT 2.0 ANGSTROMS RESOLUTION | ||||||
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 | Lionetti, C. / Guanziroli, M.G. / Frigerio, F. / Ascenzi, P. / Bolognesi, M. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1991 Title: X-ray crystal structure of the ferric sperm whale myoglobin: imidazole complex at 2.0 A resolution. Authors: Lionetti, C. / Guanziroli, M.G. / Frigerio, F. / Ascenzi, P. / Bolognesi, M. #1: Journal: J.Mol.Biol. / Year: 1989 Title: Aplysia Limacina Myoglobin. Crystallographic Analysis at 1.6 Angstroms Resolution Authors: Bolognesi, M. / Onesti, S. / Gatti, G. / Coda, A. / Ascenzi, P. / Brunori, M. #2: Journal: J.Mol.Biol. / Year: 1982 Title: Reactivity of Ferric Aplysia and Sperm Whale Myoglobins Towards Imidazole. X-Ray and Binding Study Authors: Bolognesi, M. / Cannillo, E. / Ascenzi, P. / Giacometti, G.M. / Merli, A. / Brunori, M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1mbi.cif.gz | 46.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1mbi.ent.gz | 32.6 KB | Display | PDB format |
PDBx/mmJSON format | 1mbi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1mbi_validation.pdf.gz | 822 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1mbi_full_validation.pdf.gz | 824.6 KB | Display | |
Data in XML | 1mbi_validation.xml.gz | 10.5 KB | Display | |
Data in CIF | 1mbi_validation.cif.gz | 13.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mb/1mbi ftp://data.pdbj.org/pub/pdb/validation_reports/mb/1mbi | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Atom site foot note | 1: THERE ARE LIGAND INDUCED CONFORMATIONAL CHANGES IN RESIDUES HIS 64, ARG 45 AND ASP 60. |
-Components
#1: Protein | Mass: 17234.951 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Physeter catodon (sperm whale) / References: UniProt: P02185 |
---|---|
#2: Chemical | ChemComp-SO4 / |
#3: Chemical | ChemComp-HEM / |
#4: Chemical | ChemComp-IMD / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 1.94 Å3/Da / Density % sol: 36.71 % | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | *PLUS pH: 5.75 / Method: unknown | |||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Radiation | Scattering type: x-ray |
---|---|
Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 2 Å / Num. obs: 9169 / Observed criterion σ(I): 1 |
-Processing
Software | Name: TNT / Classification: refinement | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2→10 Å /
| ||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→10 Å
| ||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 10 Å / Num. reflection all: 8822 / Rfactor all: 0.148 | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |