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- PDB-7bh5: XFEL structure of the ertapenem-derived CTX-M-15 acylenzyme after... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7bh5 | ||||||
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Title | XFEL structure of the ertapenem-derived CTX-M-15 acylenzyme after mixing for 2 sec using a piezoelectric injector (PolyPico) | ||||||
![]() | Beta-lactamase | ||||||
![]() | ANTIMICROBIAL PROTEIN / serial crystallography / beta-lactamase / antibiotic / ertapenem / XFEL | ||||||
Function / homology | ![]() beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic / membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hinchliffe, P. / Tooke, C.L. / Butryn, A. / Spencer, J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: An on-demand, drop-on-drop method for studying enzyme catalysis by serial crystallography. Authors: Butryn, A. / Simon, P.S. / Aller, P. / Hinchliffe, P. / Massad, R.N. / Leen, G. / Tooke, C.L. / Bogacz, I. / Kim, I.S. / Bhowmick, A. / Brewster, A.S. / Devenish, N.E. / Brem, J. / Kamps, J. ...Authors: Butryn, A. / Simon, P.S. / Aller, P. / Hinchliffe, P. / Massad, R.N. / Leen, G. / Tooke, C.L. / Bogacz, I. / Kim, I.S. / Bhowmick, A. / Brewster, A.S. / Devenish, N.E. / Brem, J. / Kamps, J.J.A.G. / Lang, P.A. / Rabe, P. / Axford, D. / Beale, J.H. / Davy, B. / Ebrahim, A. / Orlans, J. / Storm, S.L.S. / Zhou, T. / Owada, S. / Tanaka, R. / Tono, K. / Evans, G. / Owen, R.L. / Houle, F.A. / Sauter, N.K. / Schofield, C.J. / Spencer, J. / Yachandra, V.K. / Yano, J. / Kern, J.F. / Orville, A.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 193.8 KB | Display | ![]() |
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PDB format | ![]() | 127.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7bh3C ![]() 7bh4C ![]() 7bh6C ![]() 7bh7C ![]() 7bhkC ![]() 7bhlC ![]() 7bhmC ![]() 7bhnC ![]() 6qw8S 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: 28292.990 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-TVE / ( |
#3: Chemical | ChemComp-CL / |
#4: Chemical | ChemComp-NA / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 41.97 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / Details: 2.0 M ammonium sulphate, 0.1 M Tris 8.0 |
-Data collection
Diffraction | Mean temperature: 307 K / Serial crystal experiment: Y |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Jul 12, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2399 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→58.78 Å / Num. obs: 35730 / % possible obs: 100 % / Redundancy: 134.23 % / Biso Wilson estimate: 22.37 Å2 / CC1/2: 0.961 / R split: 0.21 / Net I/σ(I): 39.566 |
Reflection shell | Resolution: 1.55→1.58 Å / Redundancy: 48.45 % / Mean I/σ(I) obs: 0.71 / Num. unique obs: 1751 / CC1/2: 0.097 / R split: 1.232 / % possible all: 100 |
Serial crystallography measurement | Focal spot size: 1.4 µm2 / Pulse duration: 10 fsec. / Pulse energy: 450 µJ / Pulse photon energy: 10 keV |
Serial crystallography sample delivery | Description: Acoustic droplet ejection on conveyor belt with mixing using a pizoelectric injector Method: injection |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6qw8 Resolution: 1.55→31.94 Å / SU ML: 0.2419 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.597 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: 27.62 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.55→31.94 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A
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