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Yorodumi- PDB-8ebi: XFEL structure of beta lactamase microcrystals mixed with sulbact... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ebi | ||||||
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Title | XFEL structure of beta lactamase microcrystals mixed with sulbactam solution for 15ms | ||||||
Components | Beta-lactamase | ||||||
Keywords | HYDROLASE / Beta lactamase | ||||||
Function / homology | Function and homology information beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Malla, T.N. / Schmidt, M. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat Commun / Year: 2023 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ebi.cif.gz | 258.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ebi.ent.gz | 167.9 KB | Display | PDB format |
PDBx/mmJSON format | 8ebi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ebi_validation.pdf.gz | 491.5 KB | Display | wwPDB validaton report |
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Full document | 8ebi_full_validation.pdf.gz | 501.6 KB | Display | |
Data in XML | 8ebi_validation.xml.gz | 22.8 KB | Display | |
Data in CIF | 8ebi_validation.cif.gz | 34.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eb/8ebi ftp://data.pdbj.org/pub/pdb/validation_reports/eb/8ebi | HTTPS FTP |
-Related structure data
Related structure data | 8ebrC 8ec4C 8ecfC 8gcsC 8gctC 8gcvC 8gcxC 6b5xS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Mycobacterium tuberculosis (bacteria) / Gene: blaC, ERS027646_02769 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A655AHQ9, beta-lactamase #2: Chemical | ChemComp-PO4 / #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.7 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: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: MFX / Wavelength: 1.26 Å |
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: 2.65→20.86 Å / Num. obs: 41529 / % possible obs: 100 % / Redundancy: 273 % / Biso Wilson estimate: 63.35 Å2 / CC star: 0.98 / R split: 0.23 / Net I/σ(I): 4.5 |
Reflection shell | Resolution: 2.65→2.75 Å / Redundancy: 130 % / Num. unique obs: 4080 / CC star: 0.58 / R split: 3.16 / % possible all: 100 |
Serial crystallography sample delivery | Method: injection |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6b5x Resolution: 2.7→20.86 Å / SU ML: 0.5178 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.5327 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: 63 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→20.86 Å
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Refine LS restraints |
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LS refinement shell |
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