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Yorodumi- PDB-8b1w: NDM-1 metallo-beta-lactamase in complex with triazole-based inhib... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8b1w | ||||||
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Title | NDM-1 metallo-beta-lactamase in complex with triazole-based inhibitor CP35 | ||||||
Components | Beta-lactamase NDM-1 | ||||||
Keywords | HYDROLASE / Beta-lactamase / Antibiotic resistance / Beta-lactamase inhibitor | ||||||
Function / homology | Function and homology information antibiotic catabolic process / beta-lactamase / hydrolase activity / metal ion binding Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Vascon, F. / Lazzarato, L. / Bersani, M. / Gianquinto, E. / Docquier, J.D. / Spyrakis, F. / Tondi, D. / Cendron, L. | ||||||
Funding support | Italy, 1items
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Citation | Journal: Pharmaceuticals / Year: 2023 Title: Structure-Based Optimization of 1,2,4-Triazole-3-Thione Derivatives: Improving Inhibition of NDM-/VIM-Type Metallo-beta-Lactamases and Synergistic Activity on Resistant Bacteria. Authors: Bersani, M. / Failla, M. / Vascon, F. / Gianquinto, E. / Bertarini, L. / Baroni, M. / Cruciani, G. / Verdirosa, F. / Sannio, F. / Docquier, J.D. / Cendron, L. / Spyrakis, F. / Lazzarato, L. / Tondi, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8b1w.cif.gz | 105.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8b1w.ent.gz | 78.5 KB | Display | PDB format |
PDBx/mmJSON format | 8b1w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8b1w_validation.pdf.gz | 978 KB | Display | wwPDB validaton report |
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Full document | 8b1w_full_validation.pdf.gz | 980.7 KB | Display | |
Data in XML | 8b1w_validation.xml.gz | 19.9 KB | Display | |
Data in CIF | 8b1w_validation.cif.gz | 28.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b1/8b1w ftp://data.pdbj.org/pub/pdb/validation_reports/b1/8b1w | HTTPS FTP |
-Related structure data
Related structure data | 8b1zC 8b20C 6tgdS 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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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 25631.820 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: blaNDM-1, blaNDM1, E5D53_33975 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: F6IAY7 |
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-Non-polymers , 6 types, 167 molecules
#2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-CA / #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-EPE / | #7: 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: 1.95 Å3/Da / Density % sol: 36.91 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1 M HEPES, 0.1 M MOPS, pH 7.5, 0.03 M MgCl2 exahydrate, 0.03 M CaCl2 dihydrate, 12.5% v/v MPD, 12.5% w/v PEG 1000, 12.5% w/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.873 Å |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Mar 2, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.873 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→36.88 Å / Num. obs: 44671 / % possible obs: 99.7 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.194 / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 1.7→1.73 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.531 / Num. unique obs: 2328 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6TGD Resolution: 1.7→36.88 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.942 / Cross valid method: THROUGHOUT / ESU R: 0.122 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 97.83 Å2 / Biso mean: 22 Å2 / Biso min: 12.67 Å2
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Refinement step | Cycle: final / Resolution: 1.7→36.88 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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