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Yorodumi- PDB-7kiw: Crystal structure of Pseudomonas aeruginosa PBP3 in complex with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7kiw | ||||||
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Title | Crystal structure of Pseudomonas aeruginosa PBP3 in complex with zidebactam | ||||||
Components | Peptidoglycan D,D-transpeptidase FtsI | ||||||
Keywords | HYDROLASE/Inhibitor/Antibiotic / Inhibitor / cell wall / antibiotic resistance / HYDROLASE / HYDROLASE-Inhibitor-Antibiotic complex | ||||||
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 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å | ||||||
Authors | van den Akker, F. / Kumar, V. | ||||||
Citation | Journal: Mbio / Year: 2021 Title: Structural Characterization of Diazabicyclooctane beta-Lactam "Enhancers" in Complex with Penicillin-Binding Proteins PBP2 and PBP3 of Pseudomonas aeruginosa. Authors: Rajavel, M. / Kumar, V. / Nguyen, H. / Wyatt, J. / Marshall, S.H. / Papp-Wallace, K.M. / Deshpande, P. / Bhavsar, S. / Yeole, R. / Bhagwat, S. / Patel, M. / 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 | 7kiw.cif.gz | 107.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7kiw.ent.gz | 79 KB | Display | PDB format |
PDBx/mmJSON format | 7kiw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ki/7kiw ftp://data.pdbj.org/pub/pdb/validation_reports/ki/7kiw | HTTPS FTP |
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-Related structure data
Related structure data | 7kisC 7kitC 7kivC 3pbqS 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: 62933.082 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) Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 Gene: ftsI, pbpB, PA4418 / Production host: Escherichia coli (E. coli) References: UniProt: G3XD46, serine-type D-Ala-D-Ala carboxypeptidase |
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#2: Chemical | ChemComp-C8V / ( |
#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: 1.92 Å3/Da / Density % sol: 35.78 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 30% polyethylene glycol 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: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 10, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 2.49→25 Å / Num. obs: 17225 / % possible obs: 99.9 % / Redundancy: 12 % / CC1/2: 0.997 / Rmerge(I) obs: 0.182 / Net I/σ(I): 22.3 |
Reflection shell | Resolution: 2.49→2.56 Å / Redundancy: 12.8 % / Rmerge(I) obs: 1.21 / Num. unique obs: 1711 / CC1/2: 0.942 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3PBQ Resolution: 2.49→24.94 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.874 / SU B: 10.423 / SU ML: 0.236 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.729 / ESU R Free: 0.327 / 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: 121.18 Å2 / Biso mean: 46.553 Å2 / Biso min: 22.36 Å2
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Refinement step | Cycle: final / Resolution: 2.49→24.94 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.494→2.559 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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