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Open data
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Basic information
Entry | Database: PDB / ID: 5z7f | |||||||||
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Title | Horse Heart Myoglobin Mutant -V68A/I107Y-Sulfide Derivative | |||||||||
![]() | Myoglobin | |||||||||
![]() | OXYGEN STORAGE / horse heart myoglobin mutant / V68A/I107Y / sulfide derivative | |||||||||
Function / homology | ![]() 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 | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Yi, J. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Horse Heart Myoglobin Mutant -V68A/I107Y-Sulfide Derivative Authors: Yi, 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 | ![]() | 47.4 KB | Display | ![]() |
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PDB format | ![]() | 31.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 829.3 KB | Display | ![]() |
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Full document | ![]() | 830.2 KB | Display | |
Data in XML | ![]() | 9.1 KB | Display | |
Data in CIF | ![]() | 11.6 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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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 17005.479 Da / Num. of mol.: 1 / Mutation: V68A,I107Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 6 types, 62 molecules ![](data/chem/img/HEM.gif)
![](data/chem/img/H2S.gif)
![](data/chem/img/NO2.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/H2S.gif)
![](data/chem/img/NO2.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-HEM / | ||||
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#3: Chemical | ChemComp-H2S / | ||||
#4: Chemical | ChemComp-NO2 / | ||||
#5: Chemical | #6: Chemical | ChemComp-GOL / | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.77 Å3/Da / Density % sol: 30.59 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: 2.5-3.0M ammonium sulfate, 0.1M Tris / PH range: 7.0-9.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 21, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97845 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→60.38 Å / Num. obs: 8914 / % possible obs: 96.98 % / Redundancy: 3.2 % / Net I/σ(I): 15 |
Reflection shell | Resolution: 1.9→1.949 Å |
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Processing
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Refinement | Resolution: 1.9→60.38 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.904 / SU B: 3.861 / SU ML: 0.114 / Cross valid method: THROUGHOUT / ESU R: 0.192 / ESU R Free: 0.17 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.078 Å2
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Refinement step | Cycle: 1 / Resolution: 1.9→60.38 Å
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Refine LS restraints |
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