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Yorodumi- PDB-6sp6: Ultra-high Resolution Crystal Structure of the CTX-M-15 Extended-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6sp6 | ||||||
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Title | Ultra-high Resolution Crystal Structure of the CTX-M-15 Extended-Spectrum beta-Lactamase in Complex with Taniborbactam (VNRX-5133) | ||||||
Components | Beta-lactamase | ||||||
Keywords | HYDROLASE / beta-lactamase / antibiotic resistance / beta-lactam hydrolysis | ||||||
Function / homology | Function and homology information beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.1 Å | ||||||
Authors | Docquier, J.D. / Pozzi, C. / De Luca, F. / Benvenuti, M. / Mangani, S. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2020 Title: Discovery of Taniborbactam (VNRX-5133): A Broad-Spectrum Serine- and Metallo-beta-lactamase Inhibitor for Carbapenem-Resistant Bacterial Infections. Authors: Liu, B. / Trout, R.E.L. / Chu, G.H. / McGarry, D. / Jackson, R.W. / Hamrick, J.C. / Daigle, D.M. / Cusick, S.M. / Pozzi, C. / De Luca, F. / Benvenuti, M. / Mangani, S. / Docquier, J.D. / ...Authors: Liu, B. / Trout, R.E.L. / Chu, G.H. / McGarry, D. / Jackson, R.W. / Hamrick, J.C. / Daigle, D.M. / Cusick, S.M. / Pozzi, C. / De Luca, F. / Benvenuti, M. / Mangani, S. / Docquier, J.D. / Weiss, W.J. / Pevear, D.C. / Xerri, L. / Burns, C.J. #1: Journal: Antimicrob. Agents Chemother. / Year: 2019 Title: VNRX-5133 (Taniborbactam), a broad-spectrum inhibitor of serine- and metallo-beta-lactamases, restores activity of cefepime in Enterobacterales and Pseudomonas aeruginosa. Authors: Hamrick, J.C. / Docquier, J.D. / Uehara, T. / Myers, C.L. / Six, D.A. / Chatwin, C.L. / John, K.J. / Vernacchio, S.F. / Cusick, S.M. / Trout, R.E.L. / Pozzi, C. / De Luca, F. / Benvenuti, M. ...Authors: Hamrick, J.C. / Docquier, J.D. / Uehara, T. / Myers, C.L. / Six, D.A. / Chatwin, C.L. / John, K.J. / Vernacchio, S.F. / Cusick, S.M. / Trout, R.E.L. / Pozzi, C. / De Luca, F. / Benvenuti, M. / Mangani, S. / Liu, B. / Jackson, R.W. / Moeck, G. / Xerri, L. / Burns, C.J. / Pevear, D.C. / Daigle, D.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6sp6.cif.gz | 132.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6sp6.ent.gz | 99.8 KB | Display | PDB format |
PDBx/mmJSON format | 6sp6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sp/6sp6 ftp://data.pdbj.org/pub/pdb/validation_reports/sp/6sp6 | HTTPS FTP |
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-Related structure data
Related structure data | 6sp7C 4hbtS S: Starting model for refinement 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 28010.697 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: blactx-m-15 / Plasmid: pET-9a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A223A5J4, beta-lactamase |
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-Non-polymers , 5 types, 270 molecules
#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-KJK / ( | #4: Chemical | #5: Chemical | ChemComp-PGE / | #6: Water | ChemComp-HOH / | |
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-Details
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: 2.13 Å3/Da / Density % sol: 42.29 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1M Tris-HCl, 2.2-2.4M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jun 26, 2015 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.966 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.1→58.61 Å / Num. all: 96837 / Num. obs: 96837 / % possible obs: 98.9 % / Redundancy: 5.3 % / Rpim(I) all: 0.035 / Rrim(I) all: 0.083 / Rsym value: 0.075 / Net I/av σ(I): 5.3 / Net I/σ(I): 11.6 / Num. measured all: 511886 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4HBT Resolution: 1.1→58.61 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.982 / SU B: 0.643 / SU ML: 0.014 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.021 / ESU R Free: 0.022 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 190.16 Å2 / Biso mean: 12.099 Å2 / Biso min: 3.79 Å2
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Refinement step | Cycle: final / Resolution: 1.1→58.61 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.1→1.129 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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