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- PDB-7vw4: The X-ray structure of sperm whale F46C/L61C myoglobin double mutant -
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Open data
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Basic information
Entry | Database: PDB / ID: 7vw4 | ||||||
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Title | The X-ray structure of sperm whale F46C/L61C myoglobin double mutant | ||||||
![]() | Myoglobin | ||||||
![]() | OXYGEN STORAGE / SPERM WHALE myoglobin | ||||||
Function / homology | ![]() nitrite reductase activity / Oxidoreductases; Acting on other nitrogenous compounds as donors / 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 | ![]() ![]() ![]() | ||||||
![]() | Lin, Y.W. | ||||||
Funding support | ![]()
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![]() | ![]() Title: The X-ray structure of sperm whale F46C/L61C myoglobin double mutant Authors: Lin, Y.W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 54.4 KB | Display | ![]() |
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PDB format | ![]() | 32.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 854.4 KB | Display | ![]() |
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Full document | ![]() | 857.2 KB | Display | |
Data in XML | ![]() | 10.2 KB | Display | |
Data in CIF | ![]() | 13.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 101mS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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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: 17312.102 Da / Num. of mol.: 1 / Mutation: F46C, L61C Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-HEM / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.21 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: PEG 8000, Sodium cacodylate trihydrate pH 6.5, Sodium acetate trihydrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 22, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→24.01 Å / Num. obs: 27268 / % possible obs: 95.63 % / Redundancy: 13.2 % / Biso Wilson estimate: 22.61 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.08057 / Rpim(I) all: 0.02286 / Net I/σ(I): 25.39 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 13.6 % / Rmerge(I) obs: 0.6268 / Mean I/σ(I) obs: 6.15 / Num. unique obs: 2600 / Rpim(I) all: 0.1739 / % possible all: 94.34 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 101M Resolution: 1.8→24.01 Å / SU ML: 0.227 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 24.0506 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.52 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→24.01 Å
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Refine LS restraints |
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LS refinement shell |
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