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Yorodumi- PDB-1nz5: The Horse heart myoglobin variant K45E/K63E complexed with Manganese -
+Open data
-Basic information
Entry | Database: PDB / ID: 1nz5 | ||||||
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Title | The Horse heart myoglobin variant K45E/K63E complexed with Manganese | ||||||
Components | Myoglobin | ||||||
Keywords | OXYGEN STORAGE/TRANSPORT / Manganese Mn2+ horse heart myoglobin engineered metal binding site / OXYGEN STORAGE-TRANSPORT COMPLEX | ||||||
Function / homology | Function and homology information 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 ...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 | Equus caballus (horse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Hunter, C.L. / Maurus, R. / Mauk, M.R. / Lee, H. / Raven, E.L. / Tong, H. / Nguyen, N. / Smith, S. / Brayer, G.D. / Mauk, A.G. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2003 Title: Introduction and characterization of a functionally linked metal ion binding site at the exposed heme edge of myoglobin Authors: Hunter, C.L. / Maurus, R. / Mauk, M.R. / Lee, H. / Raven, E.L. / Tong, H. / Nguyen, N. / Smith, S. / Brayer, G.D. / Mauk, A.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1nz5.cif.gz | 44.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nz5.ent.gz | 30.8 KB | Display | PDB format |
PDBx/mmJSON format | 1nz5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1nz5_validation.pdf.gz | 467 KB | Display | wwPDB validaton report |
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Full document | 1nz5_full_validation.pdf.gz | 472 KB | Display | |
Data in XML | 1nz5_validation.xml.gz | 5.6 KB | Display | |
Data in CIF | 1nz5_validation.cif.gz | 7.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nz/1nz5 ftp://data.pdbj.org/pub/pdb/validation_reports/nz/1nz5 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 16983.383 Da / Num. of mol.: 1 / Mutation: K45E, K63E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Equus caballus (horse) / Gene: MB / Production host: Escherichia coli (E. coli) / References: UniProt: P68082 |
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#2: Chemical | ChemComp-MN / |
#3: Chemical | ChemComp-HEM / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.89 Å3/Da / Density % sol: 35.06 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: ammonium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 25 ℃ / pH: 7.3 | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→10 Å / Num. obs: 11392 / % possible obs: 77 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.083 |
Reflection | *PLUS Lowest resolution: 10 Å / % possible obs: 77 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→10 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber /
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Refinement step | Cycle: LAST / Resolution: 1.7→10 Å
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Refinement | *PLUS Lowest resolution: 10 Å / Rfactor Rwork: 0.175 | ||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||
Refine LS restraints | *PLUS
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