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Yorodumi- PDB-2qdt: Structural Basis for the Broad-Spectrum Inhibition of Metallo-{Be... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2qdt | ||||||
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Title | Structural Basis for the Broad-Spectrum Inhibition of Metallo-{Beta}-Lactamases: L1- IS38 Complex | ||||||
Components | Metallo-beta-lactamase L1 | ||||||
Keywords | HYDROLASE / ZN / METALLO / LACTAMASE / INHIBITOR / L1 | ||||||
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: 2 Å | ||||||
Authors | Garau, G. / Dideberg, O. | ||||||
Citation | Journal: Org.Biomol.Chem. / Year: 2008 Title: Structural basis for the broad-spectrum inhibition of metallo-beta-lactamases by thiols. Authors: Lienard, B.M. / Garau, G. / Horsfall, L. / Karsisiotis, A.I. / Damblon, C. / Lassaux, P. / Papamicael, C. / Roberts, G.C. / Galleni, M. / Dideberg, O. / Frere, J.M. / Schofield, C.J. #1: Journal: Antimicrob.Agents Chemother. / Year: 2007 Title: Competitive Inhibitors of the Cpha Metallo-{Beta}-Lactamase from Aeromonas Hydrophila Authors: Horsfall, L.E. / Garau, G. / Lienard, B.M.R. / Dideberg, O. / Schofield, C.J. / Frere, J.M. / Galleni, M. #2: Journal: J.Mol.Biol. / Year: 2005 Title: A Metallo-Beta-Lactamase Enzyme in Action: Crystal Structures of the Monozinc Carbapenemase Cpha and its Complex with Biapenem Authors: Garau, G. / Bebrone, C. / Anne, C. / Galleni, M. / Frere, J.M. / Dideberg, O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2qdt.cif.gz | 71.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2qdt.ent.gz | 51.7 KB | Display | PDB format |
PDBx/mmJSON format | 2qdt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2qdt_validation.pdf.gz | 444.6 KB | Display | wwPDB validaton report |
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Full document | 2qdt_full_validation.pdf.gz | 445.8 KB | Display | |
Data in XML | 2qdt_validation.xml.gz | 14.5 KB | Display | |
Data in CIF | 2qdt_validation.cif.gz | 21.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qd/2qdt ftp://data.pdbj.org/pub/pdb/validation_reports/qd/2qdt | HTTPS FTP |
-Related structure data
Related structure data | 2qdsC 1smlS 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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2 |
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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.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Stenotrophomonas maltophilia (bacteria) Strain: IID 1275 / Gene: L1 / Plasmid: PET26 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) PLYSS / References: UniProt: P52700, beta-lactamase | ||||||
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#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-I38 / | #5: 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: 2.5 Å3/Da / Density % sol: 51 % |
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Crystal grow | Temperature: 280 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG, AS, PH 6.50, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 100K, temperature 280K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: OTHER / Wavelength: 1.54179 / Wavelength: 1.54179 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 20, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54179 Å / Relative weight: 1 |
Reflection | Resolution: 1.86→50 Å / Num. all: 22311 / Num. obs: 21311 / % possible obs: 96.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 13.7 % / Rmerge(I) obs: 0.084 / Rsym value: 0.084 / Net I/σ(I): 28.1 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 11 % / Rmerge(I) obs: 0.404 / Mean I/σ(I) obs: 5.5 / Rsym value: 0.404 / % possible all: 94.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1SML Resolution: 2→26.54 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.953 / SU B: 3.23 / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.159 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.524 Å2
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Refinement step | Cycle: LAST / Resolution: 2→26.54 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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