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Yorodumi- PDB-2qds: Crystal Structure of the Zinc Carbapenemase CPHA in Complex with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2qds | ||||||
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Title | Crystal Structure of the Zinc Carbapenemase CPHA in Complex with the Inhibitor D-Captopril | ||||||
Components | Beta-lactamase | ||||||
Keywords | HYDROLASE / LACTAMASE / INHIBITOR / ZN | ||||||
Function / homology | Function and homology information antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / zinc ion binding Similarity search - Function | ||||||
Biological species | Aeromonas hydrophila (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 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. #3: 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2qds.cif.gz | 66.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2qds.ent.gz | 47.1 KB | Display | PDB format |
PDBx/mmJSON format | 2qds.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qd/2qds ftp://data.pdbj.org/pub/pdb/validation_reports/qd/2qds | HTTPS FTP |
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-Related structure data
Related structure data | 2qdtC 1x8gS 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: 25220.818 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aeromonas hydrophila (bacteria) / Gene: cphA / Plasmid: PUC20-CPHA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYSS / References: UniProt: P26918, beta-lactamase |
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-Non-polymers , 5 types, 196 molecules
#2: Chemical | ChemComp-ZN / | ||||||
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#3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-MCO / | #5: Chemical | #6: 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: 281 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG, AS, PH 6.50, VAPOR DIFFUSION, HANGING DROP, temperature 281K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.931 / Wavelength: 0.931 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 18, 2003 |
Radiation | Monochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.931 Å / Relative weight: 1 |
Reflection | Resolution: 1.66→58.41 Å / Num. obs: 30270 / % possible obs: 99.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.7 % / Rmerge(I) obs: 0.081 / Rsym value: 0.081 / Net I/σ(I): 17.1 |
Reflection shell | Resolution: 1.66→1.75 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.222 / Mean I/σ(I) obs: 4.4 / Rsym value: 0.222 / % possible all: 94.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1X8G Resolution: 1.66→50 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.249 / SU ML: 0.043 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.078 / ESU R Free: 0.076 / 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: 12.02 Å2
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Refinement step | Cycle: LAST / Resolution: 1.66→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.66→1.703 Å / Total num. of bins used: 20
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