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Open data
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Basic information
Entry | Database: PDB / ID: 5vzn | ||||||
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Title | Wild-type sperm whale myoglobin with nitric oxide | ||||||
![]() | Myoglobin | ||||||
![]() | OXYGEN TRANSPORT / Heme / Myoglobin / nitrosyl / nitric oxide | ||||||
Function / homology | ![]() Oxidoreductases; Acting on other nitrogenous compounds as donors / nitrite reductase activity / sarcoplasm / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / removal of superoxide radicals / oxygen carrier activity / peroxidase activity / oxygen binding / heme binding / extracellular exosome / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
Model details | This stable porphyrin-Fe(?Ea)-nitrosoalkane complex was obtained from the reaction of sperm whale ...This stable porphyrin-Fe(?Ea)-nitrosoalkane complex was obtained from the reaction of sperm whale myoglobin ferric H64A and N-hydroxyamphetamine. | ||||||
![]() | Wang, B. / Thomas, L.M. / Richter-Addo, G.B. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Nitrosyl Myoglobins and Their Nitrite Precursors: Crystal Structural and Quantum Mechanics and Molecular Mechanics Theoretical Investigations of Preferred Fe -NO Ligand Orientations in Myoglobin Distal Pockets. Authors: Wang, B. / Shi, Y. / Tejero, J. / Powell, S.M. / Thomas, L.M. / Gladwin, M.T. / Shiva, S. / Zhang, Y. / 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 | ![]() | 52.5 KB | Display | ![]() |
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PDB format | ![]() | 34.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 831.4 KB | Display | ![]() |
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Full document | ![]() | 833.3 KB | Display | |
Data in XML | ![]() | 10.5 KB | Display | |
Data in CIF | ![]() | 14.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5ut7C ![]() 5ut8C ![]() 5ut9C ![]() 5utaC ![]() 5utbC ![]() 5utcC ![]() 5utdC ![]() 5vzoC ![]() 5vzpC ![]() 5vzqC ![]() 6cf0C ![]() 2mbwS C: citing same article ( 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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1 |
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 17365.164 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 6 types, 169 molecules 










#2: Chemical | ChemComp-HEM / |
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#3: Chemical | ChemComp-NO / |
#4: Chemical | ChemComp-SO4 / |
#5: Chemical | ChemComp-NO2 / |
#6: Chemical | ChemComp-GOL / |
#7: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.84 Å3/Da / Density % sol: 33.07 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1 M Tris-Hcl, 1 mM EDTA, pH 7.4 2.56 M Ammonium Sulfate |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||
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Diffraction source | Source: ![]() | |||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 14, 2013 | |||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 1.7→26.42 Å / Num. obs: 11177 / % possible obs: 80.5 % / Redundancy: 2.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.03 / Rpim(I) all: 0.023 / Rrim(I) all: 0.038 / Net I/σ(I): 30.1 / Num. measured all: 27315 / Scaling rejects: 1 | |||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2MBW Resolution: 1.7→26.42 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.889 / SU ML: 0.064 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.137 / ESU R Free: 0.13 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 56.97 Å2 / Biso mean: 15.596 Å2 / Biso min: 8.1 Å2
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Refinement step | Cycle: final / Resolution: 1.7→26.42 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.701→1.745 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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