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Open data
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Basic information
Entry | Database: PDB / ID: 5cnb | ||||||
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Title | Ultrafast dynamics in myoglobin: 0.5 ps time delay | ||||||
![]() | Myoglobin | ||||||
![]() | OXYGEN STORAGE / serial femtosecond crystallography / time-resolved crystallography / free-electron laser / protein dynamics / carbon monoxide | ||||||
Function / homology | ![]() Oxidoreductases; Acting on other nitrogenous compounds as donors / nitrite reductase activity / oxygen transport / sarcoplasm / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / removal of superoxide radicals / oxygen carrier activity / peroxidase activity / oxygen binding / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Barends, T.R.M. / Foucar, L. / Ardevol, A. / Nass, K.J. / Aquila, A. / Botha, S. / Doak, R.B. / Falahati, K. / Hartmann, E. / Hilpert, M. ...Barends, T.R.M. / Foucar, L. / Ardevol, A. / Nass, K.J. / Aquila, A. / Botha, S. / Doak, R.B. / Falahati, K. / Hartmann, E. / Hilpert, M. / Heinz, M. / Hoffmann, M.C. / Koefinger, J. / Koglin, J. / Kovacsova, G. / Liang, M. / Milathianaki, D. / Lemke, H.T. / Reinstein, J. / Roome, C.M. / Shoeman, R.L. / Williams, G.J. / Burghardt, I. / Hummer, G. / Boutet, S. / Schlichting, I. | ||||||
![]() | ![]() Title: Direct observation of ultrafast collective motions in CO myoglobin upon ligand dissociation. Authors: Barends, T.R. / Foucar, L. / Ardevol, A. / Nass, K. / Aquila, A. / Botha, S. / Doak, R.B. / Falahati, K. / Hartmann, E. / Hilpert, M. / Heinz, M. / Hoffmann, M.C. / Kofinger, J. / Koglin, J. ...Authors: Barends, T.R. / Foucar, L. / Ardevol, A. / Nass, K. / Aquila, A. / Botha, S. / Doak, R.B. / Falahati, K. / Hartmann, E. / Hilpert, M. / Heinz, M. / Hoffmann, M.C. / Kofinger, J. / Koglin, J.E. / Kovacsova, G. / Liang, M. / Milathianaki, D. / Lemke, H.T. / Reinstein, J. / Roome, C.M. / Shoeman, R.L. / Williams, G.J. / Burghardt, I. / Hummer, G. / Boutet, S. / Schlichting, I. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 47.3 KB | Display | ![]() |
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PDB format | ![]() | 31.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5cmvSC ![]() 5cn4C ![]() 5cn5C ![]() 5cn6C ![]() 5cn7C ![]() 5cn8C ![]() 5cn9C ![]() 5cncC ![]() 5cndC ![]() 5cneC ![]() 5cnfC ![]() 5cngC ![]() 5d5rC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 16926.463 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() | ||||
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#2: Chemical | ChemComp-HEM / | ||||
#3: Chemical | #4: Chemical | ChemComp-CMO / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.85 Å3/Da / Density % sol: 33.4 % |
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Crystal grow | Temperature: 293 K / Method: batch mode / Details: 3.1 M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: Y | |||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||
Detector | Type: CS-PAD CXI-2 / Detector: PIXEL | |||||||||
Radiation | Protocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 1.8→15 Å / Num. obs: 11721 / % possible obs: 100 % / Redundancy: 148 % / Net I/σ(I): 3.9 | |||||||||
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 74 % / Mean I/σ(I) obs: 1.7 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5CMV Resolution: 1.8→14.708 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.16 / 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→14.708 Å
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Refine LS restraints |
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LS refinement shell |
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