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- PDB-7bh4: XFEL structure of apo CTX-M-15 after mixing for 0.7 sec with erta... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7bh4 | ||||||
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Title | XFEL structure of apo CTX-M-15 after mixing for 0.7 sec with ertapenem 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 | ![]() | 190.7 KB | Display | ![]() |
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PDB format | ![]() | 126.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 314.1 KB | Display | ![]() |
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Full document | ![]() | 314.2 KB | Display | |
Data in XML | ![]() | 12.7 KB | Display | |
Data in CIF | ![]() | 17.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7bh3C ![]() 7bh5C ![]() 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-SO4 / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.28 % |
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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: 303 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: 1.2406 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→58.83 Å / Num. obs: 35926 / % possible obs: 100 % / Redundancy: 114.15 % / Biso Wilson estimate: 21.29 Å2 / CC1/2: 0.949 / R split: 0.237 / Net I/σ(I): 36.063 |
Reflection shell | Resolution: 1.55→1.58 Å / Mean I/σ(I) obs: 0.86 / Num. unique obs: 1756 / CC1/2: 0.103 / R split: 1.163 |
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→32.01 Å / SU ML: 0.311 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.2598 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: 29.74 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.55→32.01 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 |
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