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Yorodumi- PDB-6y6z: Structure of Pseudomonas aeruginosa Penicillin-Binding Protein 3 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6y6z | ||||||
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Title | Structure of Pseudomonas aeruginosa Penicillin-Binding Protein 3 (PBP3) in complex with Compound 1 | ||||||
Components | Peptidoglycan D,D-transpeptidase FtsI | ||||||
Keywords | HYDROLASE / PBP3 / Penicillin Binding Proteins / Peptidoglycan production / transpeptidation | ||||||
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: 1.7 Å | ||||||
Authors | Newman, H. / Bellini, D. / Dowson, C.G. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Chem Sci / Year: 2020 Title: Demonstration of the utility of DOS-derived fragment libraries for rapid hit derivatisation in a multidirectional fashion. Authors: Kidd, S.L. / Fowler, E. / Reinhardt, T. / Compton, T. / Mateu, N. / Newman, H. / Bellini, D. / Talon, R. / McLoughlin, J. / Krojer, T. / Aimon, A. / Bradley, A. / Fairhead, M. / Brear, P. / ...Authors: Kidd, S.L. / Fowler, E. / Reinhardt, T. / Compton, T. / Mateu, N. / Newman, H. / Bellini, D. / Talon, R. / McLoughlin, J. / Krojer, T. / Aimon, A. / Bradley, A. / Fairhead, M. / Brear, P. / Diaz-Saez, L. / McAuley, K. / Sore, H.F. / Madin, A. / O'Donovan, D.H. / Huber, K.V.M. / Hyvonen, M. / von Delft, F. / Dowson, C.G. / Spring, D.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6y6z.cif.gz | 225 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6y6z.ent.gz | 176 KB | Display | PDB format |
PDBx/mmJSON format | 6y6z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6y6z_validation.pdf.gz | 765.1 KB | Display | wwPDB validaton report |
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Full document | 6y6z_full_validation.pdf.gz | 769 KB | Display | |
Data in XML | 6y6z_validation.xml.gz | 22.9 KB | Display | |
Data in CIF | 6y6z_validation.cif.gz | 34.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y6/6y6z ftp://data.pdbj.org/pub/pdb/validation_reports/y6/6y6z | HTTPS FTP |
-Related structure data
Related structure data | 6hzrS 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: 56431.324 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria) Gene: ftsI, pbpB, PA4418 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: G3XD46, serine-type D-Ala-D-Ala carboxypeptidase | ||||
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#2: Chemical | ChemComp-OEE / ~{ | ||||
#3: Chemical | #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: 2.29 Å3/Da / Density % sol: 46.38 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.8 Details: 25% (w/v) polyethylene glycol 3,350, 0.1M Bis-Tris propane pH 7.8 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: I04-1 / Wavelength: 0.9159 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 23, 2018 / Details: mirrors |
Radiation | Monochromator: silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9159 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→61.113 Å / Num. obs: 44456 / % possible obs: 95.3 % / Redundancy: 5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.16 / Rpim(I) all: 0.076 / Rrim(I) all: 0.178 / Net I/σ(I): 4.3 |
Reflection shell | Resolution: 1.7→1.819 Å / Redundancy: 1.4 % / Rmerge(I) obs: 1.241 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2223 / CC1/2: 0.65 / Rpim(I) all: 0.494 / % possible all: 67.6 |
-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: 1.7→61.11 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.925 / SU B: 12.306 / SU ML: 0.152 / SU R Cruickshank DPI: 0.3236 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.324 / ESU R Free: 0.149 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 565.63 Å2 / Biso mean: 28.026 Å2 / Biso min: 11.32 Å2
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Refinement step | Cycle: final / Resolution: 1.7→61.11 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.701→1.745 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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