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Open data
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Basic information
Entry | Database: PDB / ID: 6krc | ||||||
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Title | An X-ray structure of ferric F43Y/F46S sperm whale myoglobin | ||||||
![]() | Myoglobin | ||||||
![]() | OXYGEN STORAGE / 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 | ![]() ![]() ![]() | ||||||
![]() | Yuan, H. / Lin, Y.W. | ||||||
![]() | ![]() Title: A Catalytic Binding Site Together with a Distal Tyr in MyoglobinAffords Catalytic Efficiencies Similar to Natural Peroxidases. Authors: Zhang, P. / Yuan, H. / Xu, J. / Wang, X.J. / Gao, S.Q. / Tan, X. / 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 | ![]() | 106.6 KB | Display | ![]() |
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PDB format | ![]() | 66.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 799.4 KB | Display | ![]() |
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Full document | ![]() | 802 KB | Display | |
Data in XML | ![]() | 11 KB | Display | |
Data in CIF | ![]() | 15.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6krfC ![]() 5xkvS 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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Unit cell |
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Components
#1: Protein | Mass: 17190.855 Da / Num. of mol.: 1 / Mutation: F43Y, F46S 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: 2.2 Å3/Da / Density % sol: 44.13 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 20% PEG8000, 0.1 M NaAc, 0.1 M MES pH 6.5 |
-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: Nov 18, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 1.39→50 Å / Num. obs: 31430 / % possible obs: 99.7 % / Redundancy: 4.6 % / Biso Wilson estimate: 14.49 Å2 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.049 / Net I/σ(I): 14.7 |
Reflection shell | Resolution: 1.39→1.42 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.762 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2147 / Rpim(I) all: 0.482 / % possible all: 96.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5XKV Resolution: 1.39→30.72 Å / SU ML: 0.1146 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 14.9515
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.49 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.39→30.72 Å
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Refine LS restraints |
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LS refinement shell |
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