+Open data
-Basic information
Entry | Database: PDB / ID: 6t5y | ||||||
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Title | Crystal structure of AmpC from E.coli with Zidebactam (WCK 5107) | ||||||
Components | Beta-lactamase | ||||||
Keywords | HYDROLASE / beta lactamase / antibiotic resistance / diazabicyclooctane / DBO | ||||||
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 | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.3 Å | ||||||
Authors | Lang, P.A. / Leissing, T.M. / Schofield, C.J. / Brem, J. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Antimicrob.Agents Chemother. / Year: 2021 Title: Structural Investigations of the Inhibition of Escherichia coli AmpC beta-Lactamase by Diazabicyclooctanes. Authors: Lang, P.A. / Leissing, T.M. / Page, M.G.P. / Schofield, C.J. / Brem, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6t5y.cif.gz | 170.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6t5y.ent.gz | 132.2 KB | Display | PDB format |
PDBx/mmJSON format | 6t5y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t5/6t5y ftp://data.pdbj.org/pub/pdb/validation_reports/t5/6t5y | HTTPS FTP |
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-Related structure data
Related structure data | 6t7lC 6tbwC 6tpmC 1iemS 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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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 39587.922 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Gene: ampC, ampA, b4150, JW4111 Production host: Escherichia coli str. K-12 substr. W3110 (bacteria) References: UniProt: P00811, beta-lactamase |
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-Non-polymers , 5 types, 405 molecules
#2: Chemical | ChemComp-PEG / |
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#3: Chemical | ChemComp-C8V / ( |
#4: Chemical | ChemComp-ZN / |
#5: Chemical | ChemComp-CL / |
#6: Water | ChemComp-HOH / |
-Details
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: 2.75 Å3/Da / Density % sol: 55.3 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 24% w/v PEG6000, 0.01 ZnCl2, 0.1 M MES pH=6.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97624 Å | |||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 13, 2018 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97624 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 1.3→68.88 Å / Num. obs: 109248 / % possible obs: 100 % / Redundancy: 75.6 % / CC1/2: 1 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.014 / Rrim(I) all: 0.121 / Net I/σ(I): 26.8 / Num. measured all: 8261802 / Scaling rejects: 14345 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / % possible all: 100
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1IEM Resolution: 1.3→61.608 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 12.61 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 64.38 Å2 / Biso mean: 21.3473 Å2 / Biso min: 8.92 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.3→61.608 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %
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