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- PDB-8bkh: Carboxymyoglobin dark state for comparison with power titration a... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8bkh | ||||||
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Title | Carboxymyoglobin dark state for comparison with power titration and 23 / 101 mJ/cm2 time series | ||||||
![]() | Myoglobin | ||||||
![]() | OXYGEN STORAGE / XFEL / SFX / photolysis / pump-probe / Free-electron Laser / Serial Femtosecond Crystallography | ||||||
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. / Schlichting, I. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Influence of pump laser fluence on ultrafast myoglobin structural dynamics. Authors: Barends, T.R.M. / Gorel, A. / Bhattacharyya, S. / Schiro, G. / Bacellar, C. / Cirelli, C. / Colletier, J.P. / Foucar, L. / Grunbein, M.L. / Hartmann, E. / Hilpert, M. / Holton, J.M. / ...Authors: Barends, T.R.M. / Gorel, A. / Bhattacharyya, S. / Schiro, G. / Bacellar, C. / Cirelli, C. / Colletier, J.P. / Foucar, L. / Grunbein, M.L. / Hartmann, E. / Hilpert, M. / Holton, J.M. / Johnson, P.J.M. / Kloos, M. / Knopp, G. / Marekha, B. / Nass, K. / Nass Kovacs, G. / Ozerov, D. / Stricker, M. / Weik, M. / Doak, R.B. / Shoeman, R.L. / Milne, C.J. / Huix-Rotllant, M. / Cammarata, M. / 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 | ![]() | 49.3 KB | Display | ![]() |
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PDB format | ![]() | 32.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8bknC ![]() 8r8fC ![]() 8r8gC ![]() 8r8hC ![]() 8r8iC ![]() 8r8jC ![]() 8r8wC ![]() 8r8xC ![]() 8r8yC ![]() 8r8zC ![]() 8r90C ![]() 8r91C ![]() 8r92C ![]() 8r93C ![]() 8r94C ![]() 8r95C ![]() 8r9cC ![]() 8r9dC ![]() 8r9eC ![]() 8r9fC ![]() 8r9gC ![]() 8r9hC ![]() 8r9iC ![]() 8r9jC ![]() 8r9kC ![]() 8r9lC ![]() 8r9mC ![]() 8r9nC ![]() 8r9pC ![]() 8r9qC ![]() 8ra1C ![]() 8ra2C ![]() 8ra3C ![]() 8ra4C ![]() 8ra5C ![]() 8ra6C ![]() 8ra7C ![]() 8ra8C ![]() 8ra9C ![]() 8raaC ![]() 8rabC ![]() 8racC ![]() 8radC ![]() 8raeC ![]() 5d5rS S: Starting model for refinement C: citing same article ( |
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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: 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 / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.87 Å3/Da / Density % sol: 34.15 % |
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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: N |
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Diffraction source | Source: ![]() |
Detector | Type: CUSTOM-MADE / Detector: PIXEL / Date: May 1, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→30.67 Å / Num. obs: 27862 / % possible obs: 100 % / Redundancy: 121.4 % / Biso Wilson estimate: 15.27 Å2 / CC star: 0.982 / R split: 0.224 / Net I/σ(I): 4 |
Reflection shell | Resolution: 1.35→1.39 Å / Num. unique obs: 2319 / CC star: 0.72 / R split: 0.86 / % possible all: 99.6 |
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Processing
Software | Name: PHENIX / Version: 1.19.2_4158 / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: ![]() Starting model: 5d5r Resolution: 1.35→20.44 Å / SU ML: 0.1726 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.6231 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: 18.96 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.35→20.44 Å
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Refine LS restraints |
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LS refinement shell |
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