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- PDB-7ato: Structure of P. aeruginosa PBP3 in complex with an aryl boronic a... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7ato | ||||||
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Title | Structure of P. aeruginosa PBP3 in complex with an aryl boronic acid (Compound 2) | ||||||
![]() | Peptidoglycan D,D-transpeptidase FtsI | ||||||
![]() | HYDROLASE / D / D-transpeptidase / boron-binding / trivalency | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Newman, H. / Bellini, B. / Dowson, C.G. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 212.6 KB | Display | ![]() |
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PDB format | ![]() | 162.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 748.6 KB | Display | ![]() |
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Full document | ![]() | 756.2 KB | Display | |
Data in XML | ![]() | 22.4 KB | Display | |
Data in CIF | ![]() | 32.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7atmC ![]() 7atwC ![]() 7atxC ![]() 7au0C ![]() 7au1C ![]() 7au8C ![]() 7au9C ![]() 7aubC ![]() 7auhC ![]() 6hzrS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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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.) ![]() ![]() ![]() References: UniProt: G3XD46, serine-type D-Ala-D-Ala carboxypeptidase |
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#2: Chemical | ChemComp-RXW / ( |
#3: Chemical | ChemComp-DMS / |
#4: Chemical | ChemComp-GOL / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: 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: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 13, 2018 / Details: Mirrors |
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 |
Reflection | Resolution: 1.587→61.113 Å / Num. obs: 53748 / % possible obs: 95.5 % / Redundancy: 7.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.024 / Net I/σ(I): 15.8 |
Reflection shell | Resolution: 1.587→1.706 Å / Redundancy: 7.6 % / Rmerge(I) obs: 1.329 / Num. unique obs: 2687 / CC1/2: 0.599 / Rpim(I) all: 0.512 / % possible all: 65.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6HZR Resolution: 1.587→61.113 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.948 / WRfactor Rfree: 0.242 / WRfactor Rwork: 0.153 / SU B: 6.906 / SU ML: 0.098 / Average fsc free: 0.9054 / Average fsc work: 0.9327 / Cross valid method: FREE R-VALUE / ESU R: 0.144 / ESU R Free: 0.117 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: 41.788 Å2
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Refinement step | Cycle: LAST / Resolution: 1.587→61.113 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.587→1.628 Å
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