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- PDB-5nbk: NDM-1 metallo-beta-lactamase: a parsimonious interpretation of th... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5nbk | ||||||
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Title | NDM-1 metallo-beta-lactamase: a parsimonious interpretation of the diffraction data | ||||||
![]() | 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: Approved Drugs Containing Thiols as Inhibitors of Metallo-beta-lactamases: Strategy To Combat Multidrug-Resistant Bacteria. Authors: Klingler, F.M. / Wichelhaus, T.A. / Frank, D. / Cuesta-Bernal, J. / El-Delik, J. / Muller, H.F. / Sjuts, H. / Gottig, S. / Koenigs, A. / Pos, K.M. / Pogoryelov, D. / Proschak, E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 189 KB | Display | ![]() |
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PDB format | ![]() | 150.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 644.2 KB | Display | ![]() |
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Full document | ![]() | 646.5 KB | Display | |
Data in XML | ![]() | 19.4 KB | Display | |
Data in CIF | ![]() | 26.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5n0hC ![]() 5n0iC ![]() 5o2eC ![]() 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 43 - 271 / Label seq-ID: 16 - 244
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Components
-Protein , 1 types, 2 molecules AC
#1: Protein | Mass: 26834.170 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 119 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/P6G.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/P6G.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ZN / #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-P6G / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.75 Å3/Da / Density % sol: 55.31 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 24 % PEG 1500 AND 0.05 M TBG (SODIUM TARTRATE/BIS - TRIS/GLYCYLGLYCINE) PH 4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Sep 13, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.6→46.66 Å / Num. obs: 17411 / % possible obs: 100 % / Redundancy: 9.2 % / Net I/σ(I): 999 |
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Processing
Software | Name: REFMAC / Version: 5.8.0135 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 2.6→46.66 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.908 / SU B: 20.819 / SU ML: 0.22 / Cross valid method: FREE R-VALUE / ESU R: 0.627 / ESU R Free: 0.283 / 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: 42.719 Å2
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Refinement step | Cycle: 1 / Resolution: 2.6→46.66 Å
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Refine LS restraints |
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