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- PDB-5o2e: Crystal structure of NDM-1 in complex with hydrolyzed cefuroxime ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5o2e | |||||||||
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Title | Crystal structure of NDM-1 in complex with hydrolyzed cefuroxime - new refinement | |||||||||
![]() | Metallo-beta-lactamase type 2 | |||||||||
![]() | HYDROLASE / NDM-1 / metallo-beta-lactamase | |||||||||
Function / homology | ![]() antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / zinc ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Raczynska, J.E. / Shabalin, I.G. / Jaskolski, M. / Minor, W. / Wlodawer, A. | |||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 228.4 KB | Display | ![]() |
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PDB format | ![]() | 181.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 27 KB | Display | |
Data in CIF | ![]() | 41.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5n0hC ![]() 5n0iC ![]() 5nbkC ![]() 5o2fC ![]() 5w8wC ![]() 6ex7C C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 25631.820 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 685 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/3S0.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/3S0.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-SO4 / | #4: Chemical | #5: Chemical | Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.67 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 30% (w/v) PEG3350, 0.1M Bis-Tris pH 6.0 and 0.2 M lithium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 12, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→29.36 Å / Num. obs: 93575 / % possible obs: 98.8 % |
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Processing
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Refinement | Method to determine structure: ![]()
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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: 14.575 Å2
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Refinement step | Cycle: 1 / Resolution: 1.3→29.36 Å
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Refine LS restraints |
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