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Yorodumi- PDB-7au1: Structure of P. aeruginosa PBP3 in complex with a benzoxaborole (... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7au1 | |||||||||
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Title | Structure of P. aeruginosa PBP3 in complex with a benzoxaborole (Compound 12) | |||||||||
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 / division septum assembly / serine-type D-Ala-D-Ala carboxypeptidase activity / 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: 1.36 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 | 7au1.cif.gz | 223.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7au1.ent.gz | 171.1 KB | Display | PDB format |
PDBx/mmJSON format | 7au1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7au1_validation.pdf.gz | 759.5 KB | Display | wwPDB validaton report |
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Full document | 7au1_full_validation.pdf.gz | 767.9 KB | Display | |
Data in XML | 7au1_validation.xml.gz | 25.3 KB | Display | |
Data in CIF | 7au1_validation.cif.gz | 38 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/au/7au1 ftp://data.pdbj.org/pub/pdb/validation_reports/au/7au1 | HTTPS FTP |
-Related structure data
Related structure data | 7atmC 7atoC 7atwC 7atxC 7au0C 7au8C 7au9C 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
-Protein , 1 types, 1 molecules A
#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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-Non-polymers , 5 types, 411 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-S08 / | #5: Chemical | ChemComp-GOL / #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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Has protein modification | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 41.96 % |
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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: Apr 7, 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: 1.36→60.039 Å / Num. obs: 69775 / % possible obs: 91.7 % / Redundancy: 8.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.026 / Rrim(I) all: 0.077 / Net I/σ(I): 15.1 |
Reflection shell | Resolution: 1.36→1.491 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.85 / Num. unique obs: 3488 / Rpim(I) all: 0.381 / Rrim(I) all: 0.935 / % possible all: 62.5 |
-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: 1.36→60.039 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.951 / WRfactor Rfree: 0.199 / WRfactor Rwork: 0.143 / SU B: 3.811 / SU ML: 0.061 / Average fsc free: 0.9407 / Average fsc work: 0.9566 / Cross valid method: FREE R-VALUE / ESU R: 0.096 / ESU R Free: 0.084 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: 20.581 Å2
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Refinement step | Cycle: LAST / Resolution: 1.36→60.039 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.36→1.395 Å
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