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Yorodumi- PDB-4nq6: Bacillus cereus Zn-dependent metallo-beta-lactamase at pH 7 compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4nq6 | ||||||
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Title | Bacillus cereus Zn-dependent metallo-beta-lactamase at pH 7 complexed with compound L-CS319 | ||||||
Components | Beta-lactamase 2 | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / lactamase / metallo-beta-lactamase superfamily / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
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 | Bacillus cereus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å | ||||||
Authors | Gonzalez, J.M. / Gonzalez, M.M. / Vila, A.J. | ||||||
Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2016 Title: Cross-class metallo-beta-lactamase inhibition by bisthiazolidines reveals multiple binding modes. Authors: Hinchliffe, P. / Gonzalez, M.M. / Mojica, M.F. / Gonzalez, J.M. / Castillo, V. / Saiz, C. / Kosmopoulou, M. / Tooke, C.L. / Llarrull, L.I. / Mahler, G. / Bonomo, R.A. / Vila, A.J. / Spencer, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4nq6.cif.gz | 61.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4nq6.ent.gz | 43.3 KB | Display | PDB format |
PDBx/mmJSON format | 4nq6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4nq6_validation.pdf.gz | 447.5 KB | Display | wwPDB validaton report |
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Full document | 4nq6_full_validation.pdf.gz | 448.7 KB | Display | |
Data in XML | 4nq6_validation.xml.gz | 12.1 KB | Display | |
Data in CIF | 4nq6_validation.cif.gz | 16.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nq/4nq6 ftp://data.pdbj.org/pub/pdb/validation_reports/nq/4nq6 | HTTPS FTP |
-Related structure data
Related structure data | 5ev6C 5ev8C 5evbC 5evdC 5evkC 5ew0C 5ewaC 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 24422.902 Da / Num. of mol.: 1 / Fragment: UNP residues 36-257 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus cereus (bacteria) / Gene: blm / Plasmid: pET27b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P04190, beta-lactamase | ||||||
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#2: Chemical | #3: Chemical | ChemComp-K / | #4: Chemical | ChemComp-3R9 / ( | #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: 2.31 Å3/Da / Density % sol: 46.78 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 20% PEG3350, 180mM K2SO4, protein at 15mg/ml in 10mM Tris-HCl pH7, 50mM NaCl, 1mM DTT, 1mM Zn2SO4, vapor diffusion, hanging drop, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 1, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→40.1 Å / Num. obs: 20292 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→40.09 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.93 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 4.425 / SU ML: 0.129 / SU R Cruickshank DPI: 0.1397 / Cross valid method: THROUGHOUT / ESU R: 0.14 / ESU R Free: 0.14 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.767 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→40.09 Å
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Refine LS restraints |
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