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Yorodumi- PDB-8hxn: Crystal structure of B2 Sfh-I MBL in complex with 2-amino-5-(4-(b... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8hxn | ||||||||||||
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Title | Crystal structure of B2 Sfh-I MBL in complex with 2-amino-5-(4-(but-3-en-1-yloxy)benzyl)thiazole-4-carboxylic acid | ||||||||||||
Components | Beta-lactamase | ||||||||||||
Keywords | HYDROLASE / Beta-lactamase class B Sfh-I | ||||||||||||
Function / homology | Function and homology information antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / zinc ion binding Similarity search - Function | ||||||||||||
Biological species | Serratia fonticola (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å | ||||||||||||
Authors | Yan, Y.-H. / Zhu, K.-R. / Li, G.-B. | ||||||||||||
Funding support | China, 3items
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Citation | Journal: J.Med.Chem. / Year: 2023 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8hxn.cif.gz | 70.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8hxn.ent.gz | 48.4 KB | Display | PDB format |
PDBx/mmJSON format | 8hxn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8hxn_validation.pdf.gz | 791.2 KB | Display | wwPDB validaton report |
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Full document | 8hxn_full_validation.pdf.gz | 794 KB | Display | |
Data in XML | 8hxn_validation.xml.gz | 14.6 KB | Display | |
Data in CIF | 8hxn_validation.cif.gz | 21.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hx/8hxn ftp://data.pdbj.org/pub/pdb/validation_reports/hx/8hxn | HTTPS FTP |
-Related structure data
Related structure data | 8hx5C 8hxeC 8hxiC 8hxoC 8hxpC 8hxuC 8hxvC 8hxwC 8hy1C 8hy2C 8hy6C 8hydC 8jaoC 5ew0S 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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Unit cell |
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-Components
#1: Protein | Mass: 25947.387 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Serratia fonticola (bacteria) / Gene: sfhI / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9RMI1, beta-lactamase |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-5I6 / |
#4: Chemical | ChemComp-EOH / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.96 Å3/Da / Density % sol: 37.35 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 20-40 mM Ammonium nitrate, 1% Isopropyl alcohol, 30% (v/v) Polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 195 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1 Å |
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: 1.35→36.93 Å / Num. obs: 46148 / % possible obs: 99.7 % / Redundancy: 12.4 % / CC1/2: 1 / Net I/σ(I): 21.6 |
Reflection shell | Resolution: 1.35→1.42 Å / Num. unique obs: 6530 / CC1/2: 0.815 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5EW0 Resolution: 1.35→36.93 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 15.96 / 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: 1.35→36.93 Å
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Refine LS restraints |
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LS refinement shell |
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