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- PDB-8ebr: XFEL structure of Mycobacterium tuberculosis beta lactamase micro... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8ebr | ||||||
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Title | XFEL structure of Mycobacterium tuberculosis beta lactamase microcrystals mixed with sulbactam for 30ms | ||||||
![]() | Beta-lactamase | ||||||
![]() | HYDROLASE/Inhibitor / Beta lactamase / sulbactam / inhibitor / HYDROLASE / HYDROLASE-Inhibitor complex | ||||||
Function / homology | ![]() beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Malla, T.N. / Schmidt, M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Heterogeneity in M. tuberculosis beta-lactamase inhibition by Sulbactam. Authors: Malla, T.N. / Zielinski, K. / Aldama, L. / Bajt, S. / Feliz, D. / Hayes, B. / Hunter, M. / Kupitz, C. / Lisova, S. / Knoska, J. / Martin-Garcia, J.M. / Mariani, V. / Pandey, S. / Poudyal, I. ...Authors: Malla, T.N. / Zielinski, K. / Aldama, L. / Bajt, S. / Feliz, D. / Hayes, B. / Hunter, M. / Kupitz, C. / Lisova, S. / Knoska, J. / Martin-Garcia, J.M. / Mariani, V. / Pandey, S. / Poudyal, I. / Sierra, R.G. / Tolstikova, A. / Yefanov, O. / Yoon, C.H. / Ourmazd, A. / Fromme, P. / Schwander, P. / Barty, A. / Chapman, H.N. / Stojkovic, E.A. / Batyuk, A. / Boutet, S. / Phillips Jr., G.N. / Pollack, L. / Schmidt, M. #1: Journal: Res Sq / Year: 2023 Title: Heterogeneity in the M. tuberculosis beta-Lactamase Inhibition by Sulbactam. Authors: Schmidt, M. / Malla, T.N. / Zielinski, K. / Aldama, L. / Bajt, S. / Feliz, D. / Hayes, B. / Hunter, M. / Kupitz, C. / Lisova, S. / Knoska, J. / Martin-Garcia, J. / Mariani, V. / Pandey, S. / ...Authors: Schmidt, M. / Malla, T.N. / Zielinski, K. / Aldama, L. / Bajt, S. / Feliz, D. / Hayes, B. / Hunter, M. / Kupitz, C. / Lisova, S. / Knoska, J. / Martin-Garcia, J. / Mariani, V. / Pandey, S. / Poudyal, I. / Sierra, R. / Tolstikova, A. / Yefanov, O. / Yoon, C.H. / Ourmazd, A. / Fromme, P. / Schwander, P. / Barty, A. / Chapman, H. / Stojkovic, E. / Batyuk, A. / Boutet, S. / Phillips, G. / Pollack, L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 206.4 KB | Display | ![]() |
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PDB format | ![]() | 165.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 502.6 KB | Display | ![]() |
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Full document | ![]() | 515.6 KB | Display | |
Data in XML | ![]() | 38.1 KB | Display | |
Data in CIF | ![]() | 50.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8ebiC ![]() 8ec4C ![]() 8ecfC ![]() 8gcsC ![]() 8gctC ![]() 8gcvC ![]() 8gcxC ![]() 6b5xS 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: 28400.852 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-PO4 / #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.69 Å3/Da / Density % sol: 66.71 % |
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Crystal grow | Temperature: 300 K / Method: batch mode / pH: 4.1 / Details: 2.4 M ammonium phosphate |
-Data collection
Diffraction | Mean temperature: 300 K / Serial crystal experiment: Y |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: SLAC ePix10k 2M / Detector: PIXEL / Date: Oct 11, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.26 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→20.4 Å / Num. obs: 37864 / % possible obs: 100 % / Redundancy: 119 % / Biso Wilson estimate: 62.72 Å2 / CC star: 0.98 / R split: 0.34 / Net I/σ(I): 3.09 |
Reflection shell | Resolution: 2.95→3.06 Å / Num. unique obs: 1945 / CC star: 0.53 / R split: 3.85 / % possible all: 100 |
Serial crystallography sample delivery | Method: injection |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6b5x Resolution: 2.8→20.4 Å / SU ML: 0.641 / Cross valid method: FREE R-VALUE / σ(F): 1.33 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: 60.88 Å2 | ||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→20.4 Å
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LS refinement shell | Resolution: 2.8→2.88 Å
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