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Yorodumi- PDB-8isr: Crystal structure of extended-spectrum class A beta-lactamase, CE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8isr | ||||||
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Title | Crystal structure of extended-spectrum class A beta-lactamase, CESS-1 E166Q acylated by cefaclor | ||||||
Components | Beta-lactamase | ||||||
Keywords | HYDROLASE / extended-spectrum Class A beta-lactamase | ||||||
Function / homology | Function and homology information beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic Similarity search - Function | ||||||
Biological species | Stenotrophomonas sp. KCTC 12332 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å | ||||||
Authors | 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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Citation | Journal: Int J Antimicrob Agents / Year: 2024 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8isr.cif.gz | 151.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8isr.ent.gz | 93 KB | Display | PDB format |
PDBx/mmJSON format | 8isr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8isr_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 8isr_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 8isr_validation.xml.gz | 25.6 KB | Display | |
Data in CIF | 8isr_validation.cif.gz | 38.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/is/8isr ftp://data.pdbj.org/pub/pdb/validation_reports/is/8isr | HTTPS FTP |
-Related structure data
Related structure data | 8isoSC 8ispC 8isqC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 28652.281 Da / Num. of mol.: 2 / Mutation: E166Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Stenotrophomonas sp. KCTC 12332 (bacteria) Gene: AXG53_04720 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A126NGE0, beta-lactamase #2: Chemical | Mass: 385.823 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H16ClN3O5S / Feature type: SUBJECT OF INVESTIGATION #3: Chemical | ChemComp-EDO / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.82 % |
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Crystal grow | Temperature: 288 K / Method: microbatch Details: 0.1M 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: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1.00003 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 27, 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: 2.09→30 Å / Num. obs: 34518 / % possible obs: 99.9 % / Redundancy: 13.3 % / Biso Wilson estimate: 23.87 Å2 / CC1/2: 0.991 / Net I/σ(I): 7.4 |
Reflection shell | Resolution: 2.09→2.16 Å / Num. unique obs: 3187 / CC1/2: 0.66 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 8ISO Resolution: 2.09→29.774 Å / SU ML: 0.1953 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.6393 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: 24.81 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.09→29.774 Å
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Refine LS restraints |
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LS refinement shell |
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