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Yorodumi- PDB-6ypd: Crystal structure of AmpC from E. coli with Cyclic Boronate 3 (CB... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ypd | ||||||
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Title | Crystal structure of AmpC from E. coli with Cyclic Boronate 3 (CB3 / APC308) | ||||||
Components | Beta-lactamase | ||||||
Keywords | HYDROLASE / beta lactamase / antibiotic resistance / bicyclic boronate | ||||||
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 K-12 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å | ||||||
Authors | Lang, P.A. / Brem, J. / Schofield, C.J. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Biomolecules / Year: 2020 Title: Bicyclic Boronates as Potent Inhibitors of AmpC, the Class C beta-Lactamase from Escherichia coli . Authors: Lang, P.A. / Parkova, A. / Leissing, T.M. / Calvopina, K. / Cain, R. / Krajnc, A. / Panduwawala, T.D. / Philippe, J. / Fishwick, C.W.G. / Trapencieris, P. / 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 | 6ypd.cif.gz | 173.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ypd.ent.gz | 134.5 KB | Display | PDB format |
PDBx/mmJSON format | 6ypd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ypd_validation.pdf.gz | 760.1 KB | Display | wwPDB validaton report |
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Full document | 6ypd_full_validation.pdf.gz | 760.7 KB | Display | |
Data in XML | 6ypd_validation.xml.gz | 19 KB | Display | |
Data in CIF | 6ypd_validation.cif.gz | 29.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yp/6ypd ftp://data.pdbj.org/pub/pdb/validation_reports/yp/6ypd | HTTPS FTP |
-Related structure data
Related structure data | 6t3dC 6yenC 6yeoC 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 K-12 (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 , 7 types, 364 molecules
#2: Chemical | ChemComp-KL8 / ( | ||||||||||
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#3: Chemical | #4: Chemical | ChemComp-DMS / | #5: Chemical | #6: Chemical | ChemComp-CL / | #7: Chemical | ChemComp-ZN / | #8: 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: 2.83 Å3/Da / Density % sol: 56.48 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 25% (w/v) PEG6000, 0.01 M 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: 0.9762 Å | ||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 8, 2019 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.599→138.97 Å / Num. obs: 60941 / % possible obs: 100 % / Redundancy: 77.3 % / CC1/2: 1 / Rmerge(I) obs: 0.165 / Rpim(I) all: 0.019 / Rrim(I) all: 0.166 / Net I/σ(I): 22.1 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / % possible all: 99.9
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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: 1.6→49.134 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 19.8
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 82.06 Å2 / Biso mean: 31.0051 Å2 / Biso min: 14.68 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.6→49.134 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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