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- PDB-8isq: Crystal structure of extended-spectrum class A beta-lactamase, CE... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8isq | ||||||
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Title | Crystal structure of extended-spectrum class A beta-lactamase, CESS-1 E166Q acylated by ampicillin | ||||||
![]() | Beta-lactamase | ||||||
![]() | HYDROLASE / extended-spectrum Class A beta-lactamase | ||||||
Function / homology | ![]() beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Jeong, B.G. / Kim, M.Y. / Jeong, C.S. / Do, H.W. / Lee, J.H. / Cha, S.S. | ||||||
Funding support | 1items
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![]() | ![]() Title: Characterization of the extended substrate spectrum of the class A beta-lactamase CESS-1 from Stenotrophomonas sp. and structure-based investigation into its substrate preference. Authors: Jeong, B.G. / Kim, M.Y. / Jeong, C.S. / Do, H. / Hwang, J. / Lee, J.H. / Cha, S.S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 82.7 KB | Display | ![]() |
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PDB format | ![]() | 47.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 880.4 KB | Display | ![]() |
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Full document | ![]() | 882.5 KB | Display | |
Data in XML | ![]() | 13.7 KB | Display | |
Data in CIF | ![]() | 19.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8isoSC ![]() 8ispC ![]() 8isrC 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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1 |
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 28652.281 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: AXG53_04720 / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-ZZ7 / ( |
#3: Chemical | ChemComp-BTB / |
#4: Chemical | ChemComp-GOL / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.6 % |
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Crystal grow | Temperature: 288 K / Method: microbatch Details: 0.1 M Bis-Tris pH 6.5, 20% (w/v) polyethylene glycol (PEG) monomethyl ether (MME) 5000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 26, 2022 |
Radiation | Monochromator: DCM Si (111) Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00003 Å / Relative weight: 1 |
Reflection | Resolution: 2.24→30 Å / Num. obs: 13572 / % possible obs: 99.9 % / Redundancy: 25.1 % / Biso Wilson estimate: 33.69 Å2 / CC1/2: 0.995 / Net I/σ(I): 8.82 |
Reflection shell | Resolution: 2.24→2.31 Å / Num. unique obs: 1167 / CC1/2: 0.736 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 8ISO Resolution: 2.24→28.104 Å / SU ML: 0.249 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.5135 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.81 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.24→28.104 Å
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Refine LS restraints |
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LS refinement shell |
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