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Yorodumi- PDB-7atm: Structure of P. aeruginosa PBP3 in complex with a phenyl boronic ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7atm | ||||||
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Title | Structure of P. aeruginosa PBP3 in complex with a phenyl boronic acid (Compound 1) | ||||||
Components | Peptidoglycan D,D-transpeptidase FtsI | ||||||
Keywords | HYDROLASE / D / D-transpeptidase / boron-binding / trivalency | ||||||
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 PAO1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.582 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 | 7atm.cif.gz | 114.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7atm.ent.gz | 84.5 KB | Display | PDB format |
PDBx/mmJSON format | 7atm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/at/7atm ftp://data.pdbj.org/pub/pdb/validation_reports/at/7atm | HTTPS FTP |
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-Related structure data
Related structure data | 7atoC 7atwC 7atxC 7au0C 7au1C 7au8C 7au9C 7aubC 7auhC 6r3xS 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 / Fragment: Periplasmic domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / 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-RY2 / ( |
#4: Chemical | ChemComp-DMS / |
#5: 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: 2.5 Å3/Da / Density % sol: 50.6 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 25% (w/v) polyethylene glycol 3 350, 0.1 M Bis-Tris propane pH 8 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: I03 / Wavelength: 0.97624 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 25, 2018 / Details: Mirrors |
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97624 Å / Relative weight: 1 |
Reflection | Resolution: 1.58→59.824 Å / Num. obs: 53811 / % possible obs: 95.3 % / Redundancy: 8.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.024 / Net I/σ(I): 15.8 |
Reflection shell | Resolution: 1.58→1.715 Å / Redundancy: 8.2 % / Rmerge(I) obs: 1.413 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2692 / CC1/2: 0.542 / Rpim(I) all: 0.524 / % possible all: 62.9 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6R3X Resolution: 1.582→59.82 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.948 / SU B: 2.222 / SU ML: 0.075 / SU R Cruickshank DPI: 0.111 / Cross valid method: FREE R-VALUE / σ(F): 0 / ESU R: 0.111 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 116.54 Å2 / Biso mean: 33.059 Å2 / Biso min: 15.19 Å2
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Refinement step | Cycle: final / Resolution: 1.582→59.82 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.582→1.623 Å / Rfactor Rfree error: 0
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