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Yorodumi- PDB-6s1s: Crystal structure of AmpC from Pseudomonas aeruginosa in complex ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6s1s | ||||||
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Title | Crystal structure of AmpC from Pseudomonas aeruginosa in complex with [3-(2-carboxyvinyl)phenyl]boronic acid] inhibitor | ||||||
Components | Beta-lactamase | ||||||
Keywords | HYDROLASE / Inhibitor / Complex / 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 | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å | ||||||
Authors | Kekez, I. / Vicario, M. / Bellio, P. / Tosoni, E. / Celenza, G. / Blazquez, J. / Tondi, D. / Cendron, L. | ||||||
Citation | Journal: Antibiotics / Year: 2019 Title: Phenylboronic Acids Probing Molecular Recognition against Class A and Class C beta-lactamases. Authors: Linciano, P. / Vicario, M. / Kekez, I. / Bellio, P. / Celenza, G. / Martin-Blecua, I. / Blazquez, J. / Cendron, L. / Tondi, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6s1s.cif.gz | 90.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6s1s.ent.gz | 66.6 KB | Display | PDB format |
PDBx/mmJSON format | 6s1s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6s1s_validation.pdf.gz | 734.6 KB | Display | wwPDB validaton report |
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Full document | 6s1s_full_validation.pdf.gz | 734.4 KB | Display | |
Data in XML | 6s1s_validation.xml.gz | 16 KB | Display | |
Data in CIF | 6s1s_validation.cif.gz | 23.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s1/6s1s ftp://data.pdbj.org/pub/pdb/validation_reports/s1/6s1s | HTTPS FTP |
-Related structure data
Related structure data | 4gzbS S: Starting model for refinement |
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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
#1: Protein | Mass: 43449.223 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: ampC, EFK27_12075, RW109_RW109_01564 / Production host: Escherichia coli (E. coli) / References: UniProt: Q541D8, beta-lactamase |
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#2: Chemical | ChemComp-KRT / (~{ |
#3: Chemical | ChemComp-PO4 / |
#4: 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: 2.81 Å3/Da / Density % sol: 56.16 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.7 / Details: 1.8 M potassium phosphate buffer, pH 8.7 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97779 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 29, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97779 Å / Relative weight: 1 |
Reflection | Resolution: 1.78→46.78 Å / Num. obs: 46605 / % possible obs: 97.8 % / Redundancy: 3.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.042 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 1.78→1.81 Å / Num. unique obs: 2490 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4GZB Resolution: 1.78→46.78 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.966 / SU B: 3.02 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.099 / ESU R Free: 0.095 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.297 Å2
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Refinement step | Cycle: 1 / Resolution: 1.78→46.78 Å
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Refine LS restraints |
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