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- PDB-8hxi: Crystal structure of B3 L1 MBL in complex with 2-amino-5-(4-isopr... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8hxi | ||||||||||||
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Title | Crystal structure of B3 L1 MBL in complex with 2-amino-5-(4-isopropylbenzyl)thiazole-4-carboxylic acid | ||||||||||||
![]() | (Metallo-beta-lactamase L1 type ...) x 2 | ||||||||||||
![]() | HYDROLASE / Beta-lactamase class B L1 | ||||||||||||
Function / homology | ![]() beta-lactam antibiotic catabolic process / 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: Discovery of 2-Aminothiazole-4-carboxylic Acids as Broad-Spectrum Metallo-beta-lactamase Inhibitors by Mimicking Carbapenem Hydrolysate Binding. Authors: Yan, Y.H. / Zhang, T.T. / Li, R. / Wang, S.Y. / Wei, L.L. / Wang, X.Y. / Zhu, K.R. / Li, S.R. / Liang, G.Q. / Yang, Z.B. / Yang, L.L. / Qin, S. / 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 | ![]() | 128.9 KB | Display | ![]() |
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PDB format | ![]() | 96.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 25.8 KB | Display | |
Data in CIF | ![]() | 37.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8hx5C ![]() 8hxeC ![]() 8hxnC ![]() 8hxoC ![]() 8hxpC ![]() 8hxuC ![]() 8hxvC ![]() 8hxwC ![]() 8hy1C ![]() 8hy2C ![]() 8hy6C ![]() 8hydC ![]() 8jaoC ![]() 7o0oS S: Starting model for refinement 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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Unit cell |
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Components on special symmetry positions |
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Components
-Metallo-beta-lactamase L1 type ... , 2 types, 2 molecules AB
#1: Protein | Mass: 28512.180 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() |
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#2: Protein | Mass: 28599.258 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() |
-Non-polymers , 5 types, 415 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/5A5.gif)
![](data/chem/img/SCN.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/5A5.gif)
![](data/chem/img/SCN.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-ZN / #4: Chemical | #5: Chemical | ChemComp-SCN / #6: Chemical | ChemComp-GOL / | #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: 2.32 Å3/Da / Density % sol: 47.02 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.2M Sodium thiocyanate, 16%-22% (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 9, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.81→29.694 Å / Num. obs: 49738 / % possible obs: 99.3 % / Redundancy: 25 % / CC1/2: 1 / Net I/σ(I): 30.1 |
Reflection shell | Resolution: 1.81→1.86 Å / Redundancy: 26.5 % / Num. unique obs: 3632 / CC1/2: 0.887 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7O0O Resolution: 1.81→29.694 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.16 / Stereochemistry target values: ML
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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: 1.81→29.694 Å
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Refine LS restraints |
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LS refinement shell |
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