+Open data
-Basic information
Entry | Database: PDB / ID: 6lc7 | |||||||||
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Title | Crystal structure of AmpC Ent385 free form | |||||||||
Components | Beta-lactamase | |||||||||
Keywords | HYDROLASE / BETA-LACTAMASE / CLASS C / AMPC | |||||||||
Function / homology | Function and homology information antibiotic catabolic process / beta-lactamase activity / beta-lactamase / outer membrane-bounded periplasmic space / response to antibiotic Similarity search - Function | |||||||||
Biological species | Enterobacter cloacae (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | |||||||||
Authors | Kawai, A. / Doi, Y. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Antimicrob.Agents Chemother. / Year: 2020 Title: Structural Basis of Reduced Susceptibility to Ceftazidime-Avibactam and Cefiderocol inEnterobacter cloacaeDue to AmpC R2 Loop Deletion. Authors: Kawai, A. / McElheny, C.L. / Iovleva, A. / Kline, E.G. / Sluis-Cremer, N. / Shields, R.K. / Doi, Y. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6lc7.cif.gz | 328.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6lc7.ent.gz | 254.1 KB | Display | PDB format |
PDBx/mmJSON format | 6lc7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6lc7_validation.pdf.gz | 467.5 KB | Display | wwPDB validaton report |
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Full document | 6lc7_full_validation.pdf.gz | 469.7 KB | Display | |
Data in XML | 6lc7_validation.xml.gz | 34.6 KB | Display | |
Data in CIF | 6lc7_validation.cif.gz | 52.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lc/6lc7 ftp://data.pdbj.org/pub/pdb/validation_reports/lc/6lc7 | HTTPS FTP |
-Related structure data
Related structure data | 6lc8C 6lc9C 5xhrS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-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: 39444.188 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacter cloacae (bacteria) / Gene: CKO00_24250 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0A0Q7Z8*PLUS, beta-lactamase #2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-SO4 / #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | N | Sequence details | First MET is derived from the plasmid vector. Authors have submitted the genome sequence of E. ...First MET is derived from the plasmid vector. Authors have submitted the genome sequence of E. cloacae Ent385 to the NCBI database and WGS and BioSample IDs are assigned as WNXG00000000 and SAMN13338939, respectively. | |
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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: 2.48 Å3/Da / Density % sol: 50.49 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 1.8 M ammonium sulfate, 0.1 M MES pH 5.5 and 5% 1,4-Dioxane |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 9, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→46.9 Å / Num. obs: 149918 / % possible obs: 98.7 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 18.66 |
Reflection shell | Resolution: 1.4→1.48 Å / Rmerge(I) obs: 0.66 / Num. unique obs: 23824 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5xhr Resolution: 1.4→46.9 Å / Cross valid method: FREE R-VALUE
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Displacement parameters | Biso mean: 24.83 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→46.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.4→1.42 Å
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