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Yorodumi- PDB-7au9: Structure of P. aeruginosa PBP3 in complex with a benzoxaborole (... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7au9 | ||||||
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Title | Structure of P. aeruginosa PBP3 in complex with a benzoxaborole (Compound 14) | ||||||
Components | Peptidoglycan D,D-transpeptidase FtsI | ||||||
Keywords | HYDROLASE / D / D-transpeptidase / boron-binding / divalency | ||||||
Function / homology | Function and homology information peptidoglycan glycosyltransferase activity / serine-type D-Ala-D-Ala carboxypeptidase / FtsZ-dependent cytokinesis / serine-type D-Ala-D-Ala carboxypeptidase activity / division septum assembly / penicillin binding / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / proteolysis / plasma membrane Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.137 Å | ||||||
Authors | Newman, H. / Bellini, B. / Dowson, C.G. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: J.Med.Chem. / Year: 2021 Title: High-Throughput Crystallography Reveals Boron-Containing Inhibitors of a Penicillin-Binding Protein with Di- and Tricovalent Binding Modes. Authors: Newman, H. / Krajnc, A. / Bellini, D. / Eyermann, C.J. / Boyle, G.A. / Paterson, N.G. / McAuley, K.E. / Lesniak, R. / Gangar, M. / von Delft, F. / Brem, J. / Chibale, K. / Schofield, C.J. / Dowson, C.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7au9.cif.gz | 117.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7au9.ent.gz | 84.3 KB | Display | PDB format |
PDBx/mmJSON format | 7au9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7au9_validation.pdf.gz | 774.3 KB | Display | wwPDB validaton report |
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Full document | 7au9_full_validation.pdf.gz | 781 KB | Display | |
Data in XML | 7au9_validation.xml.gz | 20.3 KB | Display | |
Data in CIF | 7au9_validation.cif.gz | 28.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/au/7au9 ftp://data.pdbj.org/pub/pdb/validation_reports/au/7au9 | HTTPS FTP |
-Related structure data
Related structure data | 7atmC 7atoC 7atwC 7atxC 7au0C 7au1C 7au8C 7aubC 7auhC 6hzrS C: citing same article (ref.) 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: 58027.047 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 Gene: ftsI, pbpB, PA4418 / Plasmid: pET47b / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: G3XD46, serine-type D-Ala-D-Ala carboxypeptidase |
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#2: Chemical | ChemComp-GOL / |
#3: Chemical | ChemComp-S1E / |
#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: 2.17 Å3/Da / Density % sol: 43.26 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 25% (w/v) polyethylene glycol 3,350, 0.1M Bis-Tris propane pH 6 and 1% (w/v) protamine sulphate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 26, 2019 / Details: Mirrors |
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91587 Å / Relative weight: 1 |
Reflection | Resolution: 2.137→60.446 Å / Num. obs: 21028 / % possible obs: 94.1 % / Redundancy: 8.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.121 / Rpim(I) all: 0.044 / Net I/σ(I): 12.9 |
Reflection shell | Resolution: 2.137→2.341 Å / Redundancy: 7.8 % / Rmerge(I) obs: 1.311 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1052 / CC1/2: 0.582 / Rpim(I) all: 0.499 / % possible all: 67.2 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6HZR Resolution: 2.137→60.446 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.906 / SU B: 8.993 / SU ML: 0.22 / Cross valid method: FREE R-VALUE / ESU R: 0.424 / ESU R Free: 0.29 Details: Hydrogens have been added in their 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 / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.565 Å2
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Refinement step | Cycle: LAST / Resolution: 2.137→60.446 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.137→2.193 Å
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