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- PDB-6q2y: Crystal structure of NDM-1 beta-lactamase in complex with broad s... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6q2y | ||||||
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Title | Crystal structure of NDM-1 beta-lactamase in complex with broad spectrum boronic inhibitor cpd3 | ||||||
![]() | Metallo-beta-lactamase type 2 | ||||||
![]() | HYDROLASE / beta-lactamase / bacterial resistance / acyclic boronic inhibitors | ||||||
Function / homology | ![]() antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / zinc ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Maso, L. / Quotadamo, A. / Bellio, P. / Montanari, M. / Venturelli, A. / Celenza, G. / Costi, M.P. / Tondi, D. / Cendron, L. | ||||||
Funding support | ![]()
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![]() | ![]() Title: X-ray Crystallography Deciphers the Activity of Broad-Spectrum Boronic Acid beta-Lactamase Inhibitors. Authors: Cendron, L. / Quotadamo, A. / Maso, L. / Bellio, P. / Montanari, M. / Celenza, G. / Venturelli, A. / Costi, M.P. / Tondi, D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 112.7 KB | Display | ![]() |
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PDB format | ![]() | 84.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 466.1 KB | Display | ![]() |
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Full document | ![]() | 473 KB | Display | |
Data in XML | ![]() | 21.7 KB | Display | |
Data in CIF | ![]() | 31.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6ibsC ![]() 6ibvC ![]() 6q30C ![]() 6q35C ![]() 5gzuS S: Starting model for refinement 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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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 25860.133 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Missing resides correspond to unobserved regions. / Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 297 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HCQ.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HCQ.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-CA / #4: Chemical | #5: Chemical | ChemComp-EPE / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.96 Å3/Da / Density % sol: 37.11 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.3 Details: 0.3 M MgCl2 exahydrate; 0.3 M CaCl2 dihydrate; 25% w/v PEG 3350; 25% w/v MPD; 20% v/v PEG 1000; 0.1 M MES/IMIDAZOLE |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 12, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1→53.56 Å / Num. obs: 212200 / % possible obs: 97.24 % / Redundancy: 5.7 % / Biso Wilson estimate: 7.44 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.059 / Net I/σ(I): 14.12 |
Reflection shell | Resolution: 1→1.036 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.377 / Mean I/σ(I) obs: 2.15 / Num. unique obs: 16742 / CC1/2: 0.717 / % possible all: 77.39 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5GZU Resolution: 1→53.62 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.965 / SU B: 0.306 / SU ML: 0.016 / Cross valid method: THROUGHOUT / ESU R: 0.025 / ESU R Free: 0.025 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 10.13 Å2
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Refinement step | Cycle: 1 / Resolution: 1→53.62 Å
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Refine LS restraints |
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