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Yorodumi- PDB-5o2f: Crystal structure of NDM-1 in complex with hydrolyzed ampicillin ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5o2f | |||||||||
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Title | Crystal structure of NDM-1 in complex with hydrolyzed ampicillin - 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 / MOLECULAR REPLACEMENT / Resolution: 2.01 Å | |||||||||
Authors | Raczynska, J.E. / Shabalin, I.G. / Jaskolski, M. / Minor, W. / Wlodawer, 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: J. Am. Chem. Soc. / Year: 2014 Title: Structural and mechanistic insights into NDM-1 catalyzed hydrolysis of cephalosporins. Authors: Feng, H. / Ding, J. / Zhu, D. / Liu, X. / Xu, X. / Zhang, Y. / Zang, S. / Wang, D.C. / Liu, W. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5o2f.cif.gz | 118.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5o2f.ent.gz | 88.8 KB | Display | PDB format |
PDBx/mmJSON format | 5o2f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o2/5o2f ftp://data.pdbj.org/pub/pdb/validation_reports/o2/5o2f | HTTPS FTP |
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-Related structure data
Related structure data | 5n0hC 5n0iC 5nbkC 5o2eC 5w8wC 6ex7C 3q6x 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, 2 molecules AB
#1: Protein | Mass: 26045.295 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 , 6 types, 447 molecules
#2: Chemical | ChemComp-ZN / #3: Chemical | #4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-CL / | #6: Chemical | #7: 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: 1.9 Å3/Da / Density % sol: 35.34 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.8 Details: 28% (w/v) PEG3350, 0.1 M Bis-Tris, pH 5.8 and 0.2 M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 18, 2012 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.008→38.785 Å / Num. obs: 26843 / % possible obs: 99.4 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3q6x 3q6x Resolution: 2.01→38.785 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.946 / SU B: 3.774 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.187 / ESU R Free: 0.152 / 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: 20.341 Å2
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Refinement step | Cycle: 1 / Resolution: 2.01→38.785 Å
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Refine LS restraints |
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