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Open data
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Basic information
Entry | Database: PDB / ID: 7dgl | ||||||||||||
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Title | The Ni-bound dimeric structure of K78H/G80A/H82A myoglobin | ||||||||||||
![]() | Myoglobin | ||||||||||||
![]() | OXYGEN BINDING / OXYGEN STORAGE | ||||||||||||
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 | ![]() ![]() ![]() | ||||||||||||
![]() | Nagao, S. / Idomoto, A. / Shibata, N. / Higuchi, Y. / Hirota, S. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Rational design of metal-binding sites in domain-swapped myoglobin dimers. Authors: Nagao, S. / Idomoto, A. / Shibata, N. / Higuchi, Y. / Hirota, S. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 80.5 KB | Display | ![]() |
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PDB format | ![]() | 58.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.9 MB | Display | ![]() |
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Full document | ![]() | 1.9 MB | Display | |
Data in XML | ![]() | 15.3 KB | Display | |
Data in CIF | ![]() | 20.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7dgjC ![]() 7dgkC ![]() 7dgmC ![]() 7dgnC ![]() 7dgoC ![]() 3vm9S S: Starting model for refinement C: citing same article ( |
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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
#1: Protein | Mass: 16939.438 Da / Num. of mol.: 2 / Mutation: K78H, G80A, H82A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.32 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.1 M Sodium acetate, 0.1 M Tris-HCl, 25% (w/v) PEG 6,000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 26, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.91→46.98 Å / Num. obs: 23917 / % possible obs: 100 % / Redundancy: 6.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.073 / Net I/σ(I): 13.9 |
Reflection shell | Resolution: 1.91→2.02 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.919 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 3452 / CC1/2: 0.705 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3VM9 Resolution: 1.91→46.93 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.927 / SU B: 4.855 / SU ML: 0.139 / Cross valid method: THROUGHOUT / ESU R: 0.189 / ESU R Free: 0.174 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.486 Å2
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Refinement step | Cycle: 1 / Resolution: 1.91→46.93 Å
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Refine LS restraints |
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