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- PDB-8hyc: Crystal structure of B1 NDM-1 MBL in complex with 2-amino-5-(2-(t... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8hyc | ||||||||||||
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Title | Crystal structure of B1 NDM-1 MBL in complex with 2-amino-5-(2-(thiophen-2-yl)ethyl)thiazole-4-carboxylic acid | ||||||||||||
![]() | Metallo-beta-lactamase type 2 | ||||||||||||
![]() | HYDROLASE / Beta-lactamase class B NDM-1 | ||||||||||||
Function / homology | ![]() antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / zinc ion binding Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Yan, Y.-H. / Zhu, K.-R. / Li, G.-B. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: 2-Aminothiazole-4-carboxylic acids as cross-class metallo-beta-lactamase inhibitors by mimicking beta-lactam hydrolysate binding Authors: Yan, Y.-H. / Zhu, K.-R. / Yang, L.-L. / Li, G.-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 | ![]() | 185.4 KB | Display | ![]() |
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PDB format | ![]() | 148.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1021.9 KB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 22.7 KB | Display | |
Data in CIF | ![]() | 32.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8hybC 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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2 |
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Unit cell |
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Components
#1: Protein | Mass: 25574.768 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Depositor stated that they had conducted structure refinement for several times and the Rwork value was still about 0.2493, which may due to the trivial density in asymmetric units. Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-ZN / #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.97 Å3/Da / Density % sol: 37.54 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1M Bis-Tris, pH 6.0, 0.2 M Lithium sulfate, 25%-37% (v/v) Polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 195 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 X CdTe 1M / Detector: PIXEL / Date: Oct 7, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.1508→19.53 Å / Num. obs: 114363 / % possible obs: 77.6 % / Redundancy: 10.6 % / CC1/2: 0.999 / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 1.1508→1.18 Å / Num. unique obs: 1646 / CC1/2: 0.032 |
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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: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.151→19.526 Å
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Refine LS restraints |
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LS refinement shell |
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