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Yorodumi- PDB-6b6f: Beta-Lactamase, mixed with Ceftriaxone, needles crystal form, 2sec -
+Open data
-Basic information
Entry | Database: PDB / ID: 6b6f | ||||||
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Title | Beta-Lactamase, mixed with Ceftriaxone, needles crystal form, 2sec | ||||||
Components | Beta-lactamase | ||||||
Keywords | Hydrolase/ANTIBIOTIC / Beta-Lactamase / ANTIBIOTIC / Hydrolase-ANTIBIOTIC complex | ||||||
Function / homology | Function and homology information penicillinase activity / cephalosporinase activity / beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / FREE ELECTRON LASER / Resolution: 2.05 Å | ||||||
Authors | Pandey, S. / Schmidt, M. | ||||||
Funding support | United States, 1items
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Citation | Journal: BMC Biol. / Year: 2018 Title: Enzyme intermediates captured "on the fly" by mix-and-inject serial crystallography. Authors: Olmos, J.L. / Pandey, S. / Martin-Garcia, J.M. / Calvey, G. / Katz, A. / Knoska, J. / Kupitz, C. / Hunter, M.S. / Liang, M. / Oberthuer, D. / Yefanov, O. / Wiedorn, M. / Heyman, M. / Holl, M. ...Authors: Olmos, J.L. / Pandey, S. / Martin-Garcia, J.M. / Calvey, G. / Katz, A. / Knoska, J. / Kupitz, C. / Hunter, M.S. / Liang, M. / Oberthuer, D. / Yefanov, O. / Wiedorn, M. / Heyman, M. / Holl, M. / Pande, K. / Barty, A. / Miller, M.D. / Stern, S. / Roy-Chowdhury, S. / Coe, J. / Nagaratnam, N. / Zook, J. / Verburgt, J. / Norwood, T. / Poudyal, I. / Xu, D. / Koglin, J. / Seaberg, M.H. / Zhao, Y. / Bajt, S. / Grant, T. / Mariani, V. / Nelson, G. / Subramanian, G. / Bae, E. / Fromme, R. / Fung, R. / Schwander, P. / Frank, M. / White, T.A. / Weierstall, U. / Zatsepin, N. / Spence, J. / Fromme, P. / Chapman, H.N. / Pollack, L. / Tremblay, L. / Ourmazd, A. / Phillips, G.N. / Schmidt, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6b6f.cif.gz | 69 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6b6f.ent.gz | 48.6 KB | Display | PDB format |
PDBx/mmJSON format | 6b6f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b6/6b6f ftp://data.pdbj.org/pub/pdb/validation_reports/b6/6b6f | HTTPS FTP |
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-Related structure data
Related structure data | 6b5xC 6b5yC 6b68C 6b69C 6b6aC 6b6bC 6b6cC 6b6dC 6b6eC C: citing same article (ref.) |
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Similar structure data |
-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.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Strain: ATCC 25618 / H37Rv / Gene: blaC, blaA, Rv2068c, MTCY49.07c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P9WKD3, beta-lactamase |
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#2: Chemical | ChemComp-9F2 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.97 Å3/Da / Density % sol: 37.57 % |
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Crystal grow | Temperature: 293 K / Method: free interface diffustion / Details: 0.1 M sodium acetate pH 5.0, 45% PEG 1000 |
-Data collection
Diffraction | Mean temperature: 300 K |
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Diffraction source | Source: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: CXI / Wavelength: 1.3 Å |
Detector | Type: CS-PAD CXI-1 / Detector: PIXEL / Date: Sep 10, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.3 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→19.854 Å / Num. obs: 13311 / % possible obs: 100 % / Redundancy: 238 % / Net I/σ(I): 5.1 |
-Processing
Software |
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Refinement | Resolution: 2.05→19.854 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 26.51
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.05→19.854 Å
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Refine LS restraints |
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LS refinement shell |
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