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Yorodumi- PDB-1pmb: THE DETERMINATION OF THE CRYSTAL STRUCTURE OF RECOMBINANT PIG MYO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1pmb | ||||||
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Title | THE DETERMINATION OF THE CRYSTAL STRUCTURE OF RECOMBINANT PIG MYOGLOBIN BY MOLECULAR REPLACEMENT AND ITS REFINEMENT | ||||||
Components | MYOGLOBIN | ||||||
Keywords | OXYGEN STORAGE | ||||||
Function / homology | Function and homology information Intracellular oxygen transport / nitrite reductase activity / Oxidoreductases; Acting on other nitrogenous compounds as donors / sarcoplasm / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / oxygen transport / removal of superoxide radicals / peroxidase activity / oxygen carrier activity / oxygen binding ...Intracellular oxygen transport / nitrite reductase activity / Oxidoreductases; Acting on other nitrogenous compounds as donors / sarcoplasm / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / oxygen transport / removal of superoxide radicals / peroxidase activity / oxygen carrier activity / oxygen binding / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | Sus scrofa (pig) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.5 Å | ||||||
Authors | Smerdon, S.J. / Oldfield, T.J. / Dodson, E.J. / Dodson, G.G. / Hubbard, R.E. / Wilkinson, A.J. | ||||||
Citation | 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. #1: 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. / 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 | 1pmb.cif.gz | 75.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pmb.ent.gz | 56.6 KB | Display | PDB format |
PDBx/mmJSON format | 1pmb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pm/1pmb ftp://data.pdbj.org/pub/pdb/validation_reports/pm/1pmb | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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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 THE ELECTRON DENSITY MAPS. 2: HOH 5 AND HOH 18 ARE WATER MOLECULES IN THE HEME POCKET BUT THEY ARE NOT LIGATED TO THE HEME IRON. |
-Components
#1: Protein | Mass: 16983.445 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: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.61 Å3/Da / Density % sol: 65.93 % | ||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 15 ℃ / pH: 7.1 / Method: vapor diffusion, hanging dropDetails: taken from Dodson, G.(1988). Protein. Eng., 2, 233-237. | ||||||||||||||||||||
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 |
Reflection | *PLUS Highest resolution: 2.5 Å / Num. obs: 15941 / Rmerge(I) obs: 0.059 / Biso Wilson estimate: 33 Å2 / Num. measured all: 49979 |
-Processing
Software | Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 2.5→10 Å /
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Refinement step | Cycle: LAST / Resolution: 2.5→10 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 10 Å / Num. reflection obs: 14481 / Rfactor obs: 0.185 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |