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Yorodumi- PDB-6vje: Crystal structure of Pseudomonas aeruginosa penicillin-binding pr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6vje | ||||||
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Title | Crystal structure of Pseudomonas aeruginosa penicillin-binding protein 3 (PBP3) complexed with ceftobiprole | ||||||
Components | Peptidoglycan D,D-transpeptidase FtsI | ||||||
Keywords | HYDROLASE / Antibiotic target / complex | ||||||
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: 1.76 Å | ||||||
Authors | van den Akker, F. / Kumar, V. | ||||||
Citation | Journal: Antimicrob.Agents Chemother. / Year: 2020 Title: Structural Insights into Ceftobiprole Inhibition of Pseudomonas aeruginosa Penicillin-Binding Protein 3. Authors: Kumar, V. / Tang, C. / Bethel, C.R. / Papp-Wallace, K.M. / Wyatt, J. / Desarbre, E. / 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 | 6vje.cif.gz | 120.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6vje.ent.gz | 88.8 KB | Display | PDB format |
PDBx/mmJSON format | 6vje.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6vje_validation.pdf.gz | 361.2 KB | Display | wwPDB validaton report |
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Full document | 6vje_full_validation.pdf.gz | 363.4 KB | Display | |
Data in XML | 6vje_validation.xml.gz | 2 KB | Display | |
Data in CIF | 6vje_validation.cif.gz | 8.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vj/6vje ftp://data.pdbj.org/pub/pdb/validation_reports/vj/6vje | HTTPS FTP |
-Related structure data
Related structure data | 3pbqS 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, ALP65_00912, CAZ10_21230, CGU42_01090, DZ934_06595, DZ962_00565, E4V10_06485, ECC04_026610, ERJ99_003095, FCG96_14995, FLI88_02250, IPC1481_11065, IPC1482_17070, IPC165_ ...Gene: pbpB, ftsI, ftsI_2, ALP65_00912, CAZ10_21230, CGU42_01090, DZ934_06595, DZ962_00565, E4V10_06485, ECC04_026610, ERJ99_003095, FCG96_14995, FLI88_02250, IPC1481_11065, IPC1482_17070, IPC165_24935, IPC170_23205, IPC669_10550, RW109_RW109_05757 Production host: Escherichia coli (E. coli) References: UniProt: Q51504, UniProt: G3XD46*PLUS, serine-type D-Ala-D-Ala carboxypeptidase | ||||
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#2: Chemical | ChemComp-RB6 / ( | ||||
#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: 2.2 Å3/Da / Density % sol: 44.11 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / 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: SSRL / Beamline: BL14-1 / Wavelength: 1.195 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 23, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.195 Å / Relative weight: 1 |
Reflection | Resolution: 1.76→39.61 Å / Num. obs: 51816 / % possible obs: 99.8 % / Redundancy: 13.4 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 25.2 |
Reflection shell | Resolution: 1.76→1.79 Å / Rmerge(I) obs: 0.984 / Num. unique obs: 2811 / % possible all: 96.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3PBQ Resolution: 1.76→39.61 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.943 / SU B: 3.306 / SU ML: 0.102 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.131 / ESU R Free: 0.131 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: 195.22 Å2 / Biso mean: 45 Å2 / Biso min: 17.94 Å2
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Refinement step | Cycle: final / Resolution: 1.76→39.61 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.76→1.804 Å / Rfactor Rfree error: 0
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