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Yorodumi- PDB-7ly1: Crystal structure of Pseudomonas aeruginosa PBP3 in complex with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ly1 | ||||||
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Title | Crystal structure of Pseudomonas aeruginosa PBP3 in complex with vaborbactam | ||||||
Components | Peptidoglycan D,D-transpeptidase FtsI | ||||||
Keywords | HYDROLASE / PBP3 / penicillin-binding protein / boronic acid inhibitor | ||||||
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 / Resolution: 2.2 Å | ||||||
Authors | van den Akker, F. / Kumar, V. | ||||||
Funding support | 1items
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Citation | Journal: Plos One / Year: 2021 Title: Structural analysis of the boronic acid beta-lactamase inhibitor vaborbactam binding to Pseudomonas aeruginosa penicillin-binding protein 3. Authors: Kumar, V. / Viviani, S.L. / Ismail, J. / Agarwal, S. / Bonomo, R.A. / van den Akker, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ly1.cif.gz | 109.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ly1.ent.gz | 79.9 KB | Display | PDB format |
PDBx/mmJSON format | 7ly1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ly/7ly1 ftp://data.pdbj.org/pub/pdb/validation_reports/ly/7ly1 | HTTPS FTP |
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-Related structure data
Related structure data | 3pboS 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: 58329.453 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: pbpB, ftsI, ftsI_2 / Production host: Escherichia coli (E. coli) References: UniProt: Q51504, serine-type D-Ala-D-Ala carboxypeptidase |
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#2: Chemical | ChemComp-4D6 / |
#3: 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: 1.99 Å3/Da / Density % sol: 38.26 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 30% PEG 4000, 0.2 M MGCL2, 0.1 M TRIS pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9201 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 26, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9201 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→29.49 Å / Num. obs: 26281 / % possible obs: 99.8 % / Redundancy: 13.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.112 / Net I/σ(I): 15.2 |
Reflection shell | Resolution: 2.2→2.25 Å / Redundancy: 11.6 % / Rmerge(I) obs: 0.836 / Num. unique obs: 1864 / CC1/2: 0.801 / % possible all: 97.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3PBO Resolution: 2.2→27.81 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.927 / SU B: 5.818 / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.271 / ESU R Free: 0.209 / 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: 123.19 Å2 / Biso mean: 48.795 Å2 / Biso min: 28.49 Å2
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Refinement step | Cycle: final / Resolution: 2.2→27.81 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.255 Å / Rfactor Rfree error: 0
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