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- PDB-1pmb: THE DETERMINATION OF THE CRYSTAL STRUCTURE OF RECOMBINANT PIG MYO... -
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Open data
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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 | ||||||
![]() | MYOGLOBIN | ||||||
![]() | OXYGEN STORAGE | ||||||
Function / homology | ![]() Intracellular oxygen transport / nitrite reductase activity / Oxidoreductases; Acting on other nitrogenous compounds as donors / oxygen transport / sarcoplasm / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / removal of superoxide radicals / oxygen carrier activity / oxygen binding / peroxidase activity ...Intracellular oxygen transport / nitrite reductase activity / Oxidoreductases; Acting on other nitrogenous compounds as donors / oxygen transport / 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 | ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | Smerdon, S.J. / Oldfield, T.J. / Dodson, E.J. / Dodson, G.G. / Hubbard, R.E. / Wilkinson, A.J. | ||||||
![]() | ![]() 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: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 75.8 KB | Display | ![]() |
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PDB format | ![]() | 56.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 541 KB | Display | ![]() |
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Full document | ![]() | 583.1 KB | Display | |
Data in XML | ![]() | 14 KB | Display | |
Data in CIF | ![]() | 18.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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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. |
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Components
#1: Protein | Mass: 16983.445 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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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 |
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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 |