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Open data
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Basic information
Entry | Database: PDB / ID: 6f18 | ||||||
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Title | Structure of Mb NMH H64V, V68A mutant complex with EDA | ||||||
![]() | Myoglobin | ||||||
![]() | OXYGEN STORAGE / Myoglobin / Heme / N-methylhistidine | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Tinzl, M. / Hayashi, T. / Mori, T. / Hilvert, D. | ||||||
![]() | ![]() Title: Capture and characterization of a reactive haem-carbenoid complex in an artificial metalloenzyme Authors: Hayashi, T. / Tinzl, M. / Mori, T. / Krengel, U. / Proppe, J. / Soetbeer, J. / Klose, D. / Jeschke, G. / Reiher, M. / Hilvert, D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 50.1 KB | Display | ![]() |
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PDB format | ![]() | 33.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 800.7 KB | Display | ![]() |
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Full document | ![]() | 801.6 KB | Display | |
Data in XML | ![]() | 10 KB | Display | |
Data in CIF | ![]() | 13.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6f17C ![]() 6f19C ![]() 6f1aC ![]() 6g5aC ![]() 6g5bC ![]() 6g5tC ![]() 1a6kS 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: 18210.963 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-HEM / |
#3: Chemical | ChemComp-EEE / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.98 Å3/Da / Density % sol: 38.02 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1 M SPG buffer at pH 6.8-7.2 containing 28-32%(w/v) PEG1500. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 2, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→47.6 Å / Num. obs: 13995 / % possible obs: 99.8 % / Redundancy: 6.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.049 / Net I/σ(I): 20.1 |
Reflection shell | Resolution: 1.8→1.84 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.577 / Mean I/σ(I) obs: 2.8 / CC1/2: 0.877 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1A6K Resolution: 1.8→40.437 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.97 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→40.437 Å
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Refine LS restraints |
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LS refinement shell |
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