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Open data
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Basic information
Entry | Database: PDB / ID: 1npg | ||||||
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Title | MYOGLOBIN (HORSE HEART) WILD-TYPE COMPLEXED WITH NITROSOETHANE | ||||||
![]() | Myoglobin | ||||||
![]() | OXYGEN STORAGE/TRANSPORT / HEME / OXYGEN STORAGE / NITRIC OXIDE / NITROSOETHANE / MYOGLOBIN / NITROSOALKANE / OXYGEN STORAGE-TRANSPORT COMPLEX | ||||||
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 | ![]() ![]() | ||||||
![]() | Copeland, D.M. / West, A.H. / Richter-Addo, G.B. | ||||||
![]() | ![]() Title: Crystal structures of ferrous horse heart myoglobin complexed with nitric oxide and nitrosoethane. Authors: Copeland, D.M. / West, A.H. / 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 | ![]() | 48.8 KB | Display | ![]() |
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PDB format | ![]() | 32.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 820.7 KB | Display | ![]() |
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Full document | ![]() | 824.4 KB | Display | |
Data in XML | ![]() | 10.8 KB | Display | |
Data in CIF | ![]() | 14.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1npfC ![]() 1dwrS 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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Unit cell |
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Components
#1: Protein | Mass: 16983.514 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ANIMAL OXYGEN STORAGE / Source: (natural) ![]() ![]() | ||||||
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#2: Chemical | #3: Chemical | ChemComp-HEM / | #4: Chemical | ChemComp-NOE / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.56 Å3/Da / Density % sol: 20.38 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 7.4 Details: AMMONIUM SULFATE, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 100K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 11, 2002 / Details: OSMIC |
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→40 Å / Num. obs: 23424 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 2.89 % / Biso Wilson estimate: 26.6 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 24.4 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 2.76 % / Rmerge(I) obs: 0.201 / Mean I/σ(I) obs: 5.1 / % possible all: 98.2 |
Reflection | *PLUS Num. obs: 13504 / Num. measured all: 39336 |
Reflection shell | *PLUS % possible obs: 98.2 % / Num. unique obs: 1323 / Num. measured obs: 3655 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1DWR Resolution: 1.7→40 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 33.043 Å2 / ksol: 0.349798 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.4 Å2 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.76 Å / Rfactor Rfree error: 0.022 /
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Refinement | *PLUS Lowest resolution: 40 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.227 / Rfactor Rwork: 0.198 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.412 / Rfactor Rwork: 0.418 |