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- PDB-7atx: Structure of P. aeruginosa PBP3 in complex with a benzoxaborole (... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7atx | ||||||
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Title | Structure of P. aeruginosa PBP3 in complex with a benzoxaborole (Compound 4) | ||||||
![]() | Peptidoglycan D,D-transpeptidase FtsI | ||||||
![]() | HYDROLASE / D / D-transpeptidase / boron-binding / divalency | ||||||
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 | ![]() | 119.9 KB | Display | ![]() |
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PDB format | ![]() | 85.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 722.8 KB | Display | ![]() |
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Full document | ![]() | 728.5 KB | Display | |
Data in XML | ![]() | 20.6 KB | Display | |
Data in CIF | ![]() | 29.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7atmC ![]() 7atoC ![]() 7atwC ![]() 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.) ![]() ![]() Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 Gene: ftsI, pbpB, PA4418 / Plasmid: pET47b / Production host: ![]() ![]() References: UniProt: G3XD46, serine-type D-Ala-D-Ala carboxypeptidase |
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#2: Chemical | ChemComp-S1B / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.27 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 25%(w/v) polyethylene glycol 3350, 0.1M Bis-Tris propane, 1%(w/v) protamine sulphate, pH 8 |
-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: 1.795→60.879 Å / Num. obs: 44743 / % possible obs: 95.5 % / Redundancy: 7.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.021 / Net I/σ(I): 16.4 |
Reflection shell | Resolution: 1.796→1.879 Å / Redundancy: 7.6 % / Rmerge(I) obs: 1.568 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 2238 / CC1/2: 0.457 / Rpim(I) all: 0.605 / % possible all: 52.2 |
-Phasing
Phasing | Method: ![]() |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 6HZR Resolution: 1.795→60.879 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.941 / WRfactor Rfree: 0.281 / WRfactor Rwork: 0.224 / SU B: 4.166 / SU ML: 0.123 / Average fsc free: 0.8695 / Average fsc work: 0.8882 / Cross valid method: THROUGHOUT / ESU R: 0.151 / ESU R Free: 0.152 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: 50.678 Å2
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Refinement step | Cycle: LAST / Resolution: 1.795→60.879 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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