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Yorodumi- PDB-6tgd: Crystal structure of NDM-1 in complex with triazole-based inhibit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6tgd | ||||||
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Title | Crystal structure of NDM-1 in complex with triazole-based inhibitor OP31 | ||||||
Components | Metallo-beta-lactamase NDM-1 | ||||||
Keywords | HYDROLASE / New Delhi metallo-beta-lactamase | ||||||
Function / homology | Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Chem-N8Q / Metallo-beta-lactamase NDM-1 Function and homology information | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.33 Å | ||||||
Authors | Maso, L. / Spirakis, F. / Santucci, M. / Simon, C. / Docquier, J.D. / Cruciani, G. / Costi, M.P. / Tondi, D. / Cendron, L. | ||||||
Funding support | Italy, 1items
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Citation | Journal: Sci Rep / Year: 2020 Title: Virtual screening identifies broad-spectrum beta-lactamase inhibitors with activity on clinically relevant serine- and metallo-carbapenemases. Authors: Spyrakis, F. / Santucci, M. / Maso, L. / Cross, S. / Gianquinto, E. / Sannio, F. / Verdirosa, F. / De Luca, F. / Docquier, J.D. / Cendron, L. / Tondi, D. / Venturelli, A. / Cruciani, G. / Costi, M.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6tgd.cif.gz | 161 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6tgd.ent.gz | 119.3 KB | Display | PDB format |
PDBx/mmJSON format | 6tgd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6tgd_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 6tgd_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 6tgd_validation.xml.gz | 22.7 KB | Display | |
Data in CIF | 6tgd_validation.cif.gz | 33 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tg/6tgd ftp://data.pdbj.org/pub/pdb/validation_reports/tg/6tgd | HTTPS FTP |
-Related structure data
Related structure data | 6tgiC 6ibvS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 25474.627 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: not visible in the electron density / Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: blaNDM-1 / Production host: Escherichia coli (E. coli) / References: UniProt: M4JT39 #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-CA / #4: Chemical | #5: Water | ChemComp-HOH / | 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: 36.99 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.3 M MgCl2 exahydrate; 0.3 M CaCl2 dihydrate; 25% w/v PEG 3350; 25% w/v MPD; 20% v/v PEG 1000; 0.1 M MES/IMIDAZOLE pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.001 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Mar 25, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.001 Å / Relative weight: 1 |
Reflection | Resolution: 1.33→42.42 Å / Num. obs: 89075 / % possible obs: 97.4 % / Redundancy: 1.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.04 / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 1.33→1.38 Å / Rmerge(I) obs: 0.251 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 8196 / CC1/2: 0.714 / % possible all: 93.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6IBV Resolution: 1.33→42.42 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.962 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.071 / ESU R Free: 0.061 / Details: 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 66.19 Å2 / Biso mean: 19.037 Å2 / Biso min: 8.97 Å2
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Refinement step | Cycle: final / Resolution: 1.33→42.42 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.332→1.367 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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