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Yorodumi- PDB-6ex7: Crystal structure of NDM-1 metallo-beta-lactamase in complex with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ex7 | ||||||
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Title | Crystal structure of NDM-1 metallo-beta-lactamase in complex with Cd ions and a hydrolyzed beta-lactam ligand - new refinement | ||||||
Components | Metallo-beta-lactamase type 2 | ||||||
Keywords | HYDROLASE / NDM-1 / metallo-beta-lactamase | ||||||
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 / Resolution: 1.95 Å | ||||||
Authors | Kim, Y. / Raczynska, J.E. / Shabalin, I.G. / Jaskolski, M. / Minor, W. / Wlodawer, A. / Tesar, C. / Jedrzejczak, R. / Babnigg, J. / Mire, J. ...Kim, Y. / Raczynska, J.E. / Shabalin, I.G. / Jaskolski, M. / Minor, W. / Wlodawer, A. / Tesar, C. / Jedrzejczak, R. / Babnigg, J. / Mire, J. / Sacchettini, J. / Joachimiak, A. | ||||||
Funding support | Poland, 1items
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Citation | Journal: Drug Resist. Updat. / Year: 2018 Title: A close look onto structural models and primary ligands of metallo-beta-lactamases. Authors: Raczynska, J.E. / Shabalin, I.G. / Minor, W. / Wlodawer, A. / Jaskolski, M. #1: Journal: FASEB J. / Year: 2013 Title: NDM-1, the ultimate promiscuous enzyme: substrate recognition and catalytic mechanism. Authors: Kim, Y. / Cunningham, M.A. / Mire, J. / Tesar, C. / Sacchettini, J. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ex7.cif.gz | 197.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ex7.ent.gz | 155.7 KB | Display | PDB format |
PDBx/mmJSON format | 6ex7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ex/6ex7 ftp://data.pdbj.org/pub/pdb/validation_reports/ex/6ex7 | HTTPS FTP |
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-Related structure data
Related structure data | 5n0hC 5n0iC 5nbkC 5o2eC 5o2fC 5w8wC 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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2 |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ILE / Beg label comp-ID: ILE / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 31 - 269 / Label seq-ID: 4 - 242
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 25717.914 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 |
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-Non-polymers , 7 types, 192 molecules
#2: Chemical | ChemComp-CD / #3: Chemical | #4: Chemical | Mass: 189.189 Da / Num. of mol.: 2 / Source method: obtained synthetically #5: Chemical | ChemComp-PG4 / | #6: Chemical | ChemComp-TOE / | #7: Chemical | ChemComp-EDO / | #8: 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: 2.05 Å3/Da / Density % sol: 39.97 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop Details: 0.2 M ammonium sulfate, 0.1 M Bis-Tris pH 5.5, 25 % PEG 3350, 5 mM CdCl2,10 mM faropenum, temperature 289K PH range: 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97934 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 8, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→74.2 Å / Num. obs: 27008 / % possible obs: 91.72 % / Redundancy: 2.9 % / Net I/σ(I): 15.6 |
Reflection shell | Resolution: 1.95→2 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 2.2 / % possible all: 66 |
-Processing
Software |
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Refinement | Resolution: 1.95→74.2 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.91 / SU B: 9.225 / SU ML: 0.131 / Cross valid method: FREE R-VALUE / ESU R: 0.221 / ESU R Free: 0.171 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.627 Å2
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Refinement step | Cycle: 1 / Resolution: 1.95→74.2 Å
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Refine LS restraints |
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