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Open data
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Basic information
Entry | Database: PDB / ID: 3vau | ||||||
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Title | Myoglobin nitrite structure: nitriheme modified | ||||||
![]() | Myoglobin | ||||||
![]() | OXYGEN TRANSPORT / myoglobin / nitrite / nitriheme | ||||||
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. / Richter-Addo, G.B. | ||||||
![]() | ![]() Title: Unveiling the three-dimensional structure of the green pigment of nitrite-cured meat Authors: Yi, J. / Richter-Addo, G.B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 47.7 KB | Display | ![]() |
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PDB format | ![]() | 32.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 785.5 KB | Display | ![]() |
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Full document | ![]() | 788.4 KB | Display | |
Data in XML | ![]() | 9.6 KB | Display | |
Data in CIF | ![]() | 12.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1dwrS S: Starting model for refinement |
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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
#1: Protein | Mass: 16983.514 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#2: Chemical | ChemComp-NTE / [ |
#3: Chemical | ChemComp-NO2 / |
#4: Chemical | ChemComp-SO4 / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.78 Å3/Da / Density % sol: 30.95 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: ammonium sulfate, 100mM TrisHCl, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 23, 2010 / Details: Osmic |
Radiation | Monochromator: Osmic mirrors / 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→26.34 Å / Num. all: 13478 / Num. obs: 13475 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.87 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 3.76 % / Rmerge(I) obs: 0.062 / Mean I/σ(I) obs: 3.4 / Num. unique all: 1362 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1DWR Resolution: 1.7→26.34 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.937 / SU B: 2.387 / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(I): 2 / ESU R: 0.126 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.304 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→26.34 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20
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