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Yorodumi- PDB-1myj: DISTAL POLARITY IN LIGAND BINDING TO MYOGLOBIN: STRUCTURAL AND FU... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1myj | ||||||
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Title | DISTAL POLARITY IN LIGAND BINDING TO MYOGLOBIN: STRUCTURAL AND FUNCTIONAL CHARACTERIZATION OF A THREONINE68(E11) MUTANT | ||||||
Components | MYOGLOBIN | ||||||
Keywords | OXYGEN STORAGE | ||||||
Function / homology | Function and homology information Intracellular oxygen transport / Oxidoreductases; Acting on other nitrogenous compounds as donors / nitrite reductase activity / oxygen transport / sarcoplasm / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / removal of superoxide radicals / oxygen carrier activity / peroxidase activity / oxygen binding ...Intracellular oxygen transport / Oxidoreductases; Acting on other nitrogenous compounds as donors / nitrite reductase activity / oxygen transport / sarcoplasm / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / removal of superoxide radicals / oxygen carrier activity / peroxidase activity / oxygen binding / heme binding / extracellular exosome / metal ion binding Similarity search - Function | ||||||
Biological species | Sus scrofa (pig) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.9 Å | ||||||
Authors | Smerdon, S.J. / Oldfield, T.J. / Wilkinson, A.J. / Dauter, Z. / Petratos, K. / Wilson, K.S. | ||||||
Citation | Journal: Biochemistry / Year: 1991 Title: Distal pocket polarity in ligand binding to myoglobin: structural and functional characterization of a threonine68(E11) mutant. Authors: Smerdon, S.J. / Dodson, G.G. / Wilkinson, A.J. / Gibson, Q.H. / Blackmore, R.S. / Carver, T.E. / Olson, J.S. #1: Journal: Acta Crystallogr.,Sect.B / Year: 1990 Title: Determination of the Crystal Structure of Recombinant Pig Myoglobin by Molecular Replacement and its Refinement Authors: Smerdon, S.J. / Oldfield, T.J. / Dodson, E.J. / Dodson, G.G. / Hubbard, R.E. / Wilkinson, A.J. #2: Journal: Protein Eng. / Year: 1988 Title: Apomyoglobin as a Molecular Recognition Surface: Expression, Reconstitution and Crystallisation of Recombinant Porcine Myoglobin in Escherichia Coli Authors: Dodson, G.G. / Hubbard, R.E. / Oldfield, T.J. / Smerdon, S.J. / Wilkinson, A.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1myj.cif.gz | 78.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1myj.ent.gz | 58.5 KB | Display | PDB format |
PDBx/mmJSON format | 1myj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1myj_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 1myj_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 1myj_validation.xml.gz | 20.4 KB | Display | |
Data in CIF | 1myj_validation.cif.gz | 26 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/my/1myj ftp://data.pdbj.org/pub/pdb/validation_reports/my/1myj | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Atom site foot note | 1: RESIDUES 152 AND 153 ARE DISORDERED AND NOT DEFINED IN DENSITY MAPS. 2: HOH 57 AND 72 ARE WATER MOLECULES IN THE HAEM POCKET AND LIGATED TO THE HAEM IRON. |
-Components
#1: Protein | Mass: 16985.418 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sus scrofa (pig) / References: UniProt: P02189 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.56 Å3/Da / Density % sol: 65.43 % | ||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 15 ℃ / pH: 7.1 / Method: vapor diffusion, hanging drop / Details: by Vapor diffusion, hanging drop, and in batch | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
-Processing
Software | Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 1.9→7 Å /
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Refinement step | Cycle: LAST / Resolution: 1.9→7 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 7 Å / Num. reflection obs: 35296 / Rfactor obs: 0.207 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |