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Yorodumi- PDB-5dpx: 1,2,4-Triazole-3-thione compounds as inhibitors of L1, di-zinc me... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5dpx | ||||||
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Title | 1,2,4-Triazole-3-thione compounds as inhibitors of L1, di-zinc metallo-beta-lactamases. | ||||||
Components | Metallo-beta-lactamase L1 type 3 | ||||||
Keywords | HYDROLASE / METALLO / ZN / LACTAMASE | ||||||
Function / homology | Function and homology information beta-lactam antibiotic catabolic process / antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / zinc ion binding Similarity search - Function | ||||||
Biological species | Stenotrophomonas maltophilia (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Nauton, L. / Garau, G. / Khan, R. / Dideberg, O. | ||||||
Citation | Journal: ChemMedChem / Year: 2017 Title: 1,2,4-Triazole-3-thione Compounds as Inhibitors of Dizinc Metallo-beta-lactamases. Authors: Sevaille, L. / Gavara, L. / Bebrone, C. / De Luca, F. / Nauton, L. / Achard, M. / Mercuri, P. / Tanfoni, S. / Borgianni, L. / Guyon, C. / Lonjon, P. / Turan-Zitouni, G. / Dzieciolowski, J. / ...Authors: Sevaille, L. / Gavara, L. / Bebrone, C. / De Luca, F. / Nauton, L. / Achard, M. / Mercuri, P. / Tanfoni, S. / Borgianni, L. / Guyon, C. / Lonjon, P. / Turan-Zitouni, G. / Dzieciolowski, J. / Becker, K. / Benard, L. / Condon, C. / Maillard, L. / Martinez, J. / Frere, J.M. / Dideberg, O. / Galleni, M. / Docquier, J.D. / Hernandez, J.F. #1: Journal: Antimicrob.Agents Chemother. / Year: 2004 Title: Update Of The Standard Numbering Scheme For Class B Beta-Lactamases Authors: Garau, G. / Garcia-Saez, I. / Bebrone, C. / Anne, C. / Mercuri, P. / Galleni, M. / Frere, J.-M. / Dideberg, O. #2: Journal: Embo J. / Year: 1995 Title: The 3-D Structure Of A Zinc Metallo-Beta-Lactamase From Bacillus Cereus Reveals A New Type Of Protein Fold Authors: Carfi, A. / Pares, S. / Duee, E. / Galleni, M. / Duez, C. / Frere, J.-M. / Dideberg, O. #3: Journal: J.Mol.Biol. / Year: 2008 Title: Structural Insights Into The Design Of Inhibitors For The L1 Metallo-Beta-Lactamase From Stenotrophomonas Maltophilia. Authors: Nauton, L. / Kahn, R. / Garau, G. / Hernandez, J.F. / Dideberg, O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5dpx.cif.gz | 130.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5dpx.ent.gz | 99.8 KB | Display | PDB format |
PDBx/mmJSON format | 5dpx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5dpx_validation.pdf.gz | 455.8 KB | Display | wwPDB validaton report |
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Full document | 5dpx_full_validation.pdf.gz | 460.9 KB | Display | |
Data in XML | 5dpx_validation.xml.gz | 26.7 KB | Display | |
Data in CIF | 5dpx_validation.cif.gz | 39.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dp/5dpx ftp://data.pdbj.org/pub/pdb/validation_reports/dp/5dpx | HTTPS FTP |
-Related structure data
Related structure data | 2hb9S S: Starting model for refinement |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 28740.453 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Stenotrophomonas maltophilia (bacteria) Cellular location: PERIPLASM / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: P52700, beta-lactamase #2: Chemical | ChemComp-ZN / #3: Chemical | #4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | |
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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: 2.73 Å3/Da / Density % sol: 54.93 % |
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Crystal grow | Temperature: 281 K / Method: vapor diffusion, hanging drop / pH: 7.75 Details: 1.8M AMMONIUM SULFATE, 0.1M HEPES, PH7.75, 1.5% V/V PEG 400, VAPOR DIFFUSION, HANGING DROP. PH range: 7.75 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Mar 15, 2006 / Details: Xenocs multilayers mirror |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→19.85 Å / Num. obs: 53574 / % possible obs: 97.2 % / Observed criterion σ(I): 2 / Redundancy: 6.8 % / Rmerge(I) obs: 0.109 / Rsym value: 0.109 / Net I/σ(I): 12.2 |
Reflection shell | Resolution: 1.85→1.95 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.385 / Mean I/σ(I) obs: 4.6 / Rsym value: 0.385 / % possible all: 97.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2HB9 Resolution: 1.85→19.851 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.28 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→19.851 Å
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Refine LS restraints |
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LS refinement shell |
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