+Open data
-Basic information
Entry | Database: PDB / ID: 4eyf | ||||||
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Title | Crystal structure of NDM-1 bound to hydrolyzed benzylpenicillin | ||||||
Components | Beta-lactamase NDM-1 | ||||||
Keywords | Hydrolase/antibiotic / Metallo Beta Lactamase / antibiotic / Hydrolase-antibiotic 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 | Klebsiella pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Strynadka, N.C.J. / King, D.T. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2012 Title: New Delhi Metallo-Beta-Lactamase: Structural Insights into Beta-Lactam Recognition and Inhibition Authors: King, D.T. / Worrall, L.J. / Gruninger, R. / Strynadka, N.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4eyf.cif.gz | 110.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4eyf.ent.gz | 84.6 KB | Display | PDB format |
PDBx/mmJSON format | 4eyf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ey/4eyf ftp://data.pdbj.org/pub/pdb/validation_reports/ey/4eyf | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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Details | It is uncertain whether the biologically active form is monomeric or dimeric |
-Components
#1: Protein | Mass: 28527.428 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: blaNDM-1 / Production host: Escherichia coli (E. coli) / References: UniProt: C7C422, beta-lactamase #2: Chemical | #3: Chemical | ChemComp-ZN / #4: Water | ChemComp-HOH / | Nonpolymer details | HYDROLYSIS | |
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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: 1.82 Å3/Da / Density % sol: 32.58 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.2M MgCl2, 25% PEG3350, 0.1M bis-tris, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1 |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Nov 22, 2011 |
Radiation | Monochromator: toroidal focusing mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→29.7 Å / Num. all: 39550 / Num. obs: 39036 / % possible obs: 98.7 % / Observed criterion σ(I): -3 |
Reflection shell | Resolution: 1.8→1.9 Å / % possible all: 97.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→29.7 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.927 / SU B: 2.296 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.119 / 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.505 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→29.7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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