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Yorodumi- PDB-6r42: Structure of R504C mutant of Pseudomonas aeruginosa Penicillin-Bi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6r42 | ||||||
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Title | Structure of R504C mutant of Pseudomonas aeruginosa Penicillin-Binding Protein 3 (PBP3) in complex with piperacillin | ||||||
Components | Peptidoglycan D,D-transpeptidase FtsI | ||||||
Keywords | HYDROLASE / penicillin-binding protein / peptidoglycan / Transpeptidase | ||||||
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: 1.72 Å | ||||||
Authors | Bellini, D. / Dowson, C.G. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: J.Mol.Biol. / Year: 2019 Title: Novel and Improved Crystal Structures of H. influenzae, E. coli and P. aeruginosa Penicillin-Binding Protein 3 (PBP3) and N. gonorrhoeae PBP2: Toward a Better Understanding of beta-Lactam ...Title: Novel and Improved Crystal Structures of H. influenzae, E. coli and P. aeruginosa Penicillin-Binding Protein 3 (PBP3) and N. gonorrhoeae PBP2: Toward a Better Understanding of beta-Lactam Target-Mediated Resistance. Authors: Bellini, D. / Koekemoer, L. / Newman, H. / Dowson, C.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6r42.cif.gz | 117.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6r42.ent.gz | 87.4 KB | Display | PDB format |
PDBx/mmJSON format | 6r42.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6r42_validation.pdf.gz | 764 KB | Display | wwPDB validaton report |
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Full document | 6r42_full_validation.pdf.gz | 774.3 KB | Display | |
Data in XML | 6r42_validation.xml.gz | 22.1 KB | Display | |
Data in CIF | 6r42_validation.cif.gz | 31 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r4/6r42 ftp://data.pdbj.org/pub/pdb/validation_reports/r4/6r42 | HTTPS FTP |
-Related structure data
Related structure data | 6hzjC 6hzoC 6hzqC 6hzrC 6i1eC 6i1iC 6r3xC 6r40C 3oc2S 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: 57972.992 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 (E. coli) References: UniProt: G3XD46, serine-type D-Ala-D-Ala carboxypeptidase |
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#2: Chemical | ChemComp-JPP / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.69 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 25% (w/v) polyethylene glycol 3 350, 0.1 M 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 / Wavelength: 0.98 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 4, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.72→54.23 Å / Num. obs: 54141 / % possible obs: 100 % / Redundancy: 11.5 % / Net I/σ(I): 13.8 |
Reflection shell | Resolution: 1.72→1.75 Å / Num. unique obs: 2641 / CC1/2: 0.5 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3OC2 Resolution: 1.72→54.2 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.934 / SU B: 4.176 / SU ML: 0.123 / Cross valid method: THROUGHOUT / ESU R: 0.125 / ESU R Free: 0.124 / Details: HYDROGENS HAVE BEEN ADDED IN THE 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.939 Å2
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Refinement step | Cycle: 1 / Resolution: 1.72→54.2 Å
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Refine LS restraints |
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