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Open data
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Basic information
Entry | Database: PDB / ID: 8v9h | ||||||
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Title | GES-5-NA-1-157 complex | ||||||
![]() | beta-lactamase | ||||||
![]() | HYDROLASE / class A beta-lactamase / carbapenemase / meropenem / antibiotic resistance | ||||||
Function / homology | ![]() beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Smith, C.A. / Stewart, N.K. / Vakulenko, S.B. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Restricted Rotational Flexibility of the C5 alpha-Methyl-Substituted Carbapenem NA-1-157 Leads to Potent Inhibition of the GES-5 Carbapenemase. Authors: Stewart, N.K. / Toth, M. / Quan, P. / Beer, M. / Buynak, J.D. / Smith, C.A. / Vakulenko, S.B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 225.3 KB | Display | ![]() |
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PDB format | ![]() | 179.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 994.8 KB | Display | ![]() |
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Full document | ![]() | 997.2 KB | Display | |
Data in XML | ![]() | 25.2 KB | Display | |
Data in CIF | ![]() | 36.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8v9gC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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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: 31222.465 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 6 types, 398 molecules ![](data/chem/img/Y33.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/IOD.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/IOD.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-EDO / #4: Chemical | #5: Chemical | ChemComp-CA / | #6: Chemical | ChemComp-CL / #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.52 % |
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Crystal grow | Temperature: 277 K / Method: batch mode Details: Crystallized spontaneously from 20 mM HEPES. Protein concentration 15 mg/ml |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 12, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→38.5 Å / Num. obs: 87364 / % possible obs: 99.9 % / Redundancy: 9.5 % / CC1/2: 0.999 / Rpim(I) all: 0.031 / Rrim(I) all: 0.094 / Net I/σ(I): 15.2 |
Reflection shell | Resolution: 1.5→1.53 Å / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4276 / CC1/2: 0.803 / Rpim(I) all: 0.416 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→38.5 Å
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Refine LS restraints |
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LS refinement shell |
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