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Yorodumi- PDB-4fsf: Crystal structure of Pseudomonas aeruginosa PBP3 complexed with c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4fsf | ||||||
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Title | Crystal structure of Pseudomonas aeruginosa PBP3 complexed with compound 14 | ||||||
Components | Penicillin-binding protein 3 | ||||||
Keywords | PENICILLIN-BINDING PROTEIN/ANTIBIOTIC / penicillin binding protein / PENICILLIN-BINDING PROTEIN-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 / plasma membrane => GO:0005886 / penicillin binding / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape ...peptidoglycan glycosyltransferase activity / serine-type D-Ala-D-Ala carboxypeptidase / FtsZ-dependent cytokinesis / division septum assembly / serine-type D-Ala-D-Ala carboxypeptidase activity / plasma membrane => GO:0005886 / 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 | Han, S. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2012 Title: Novel monobactams utilizing a siderophore uptake mechanism for the treatment of gram-negative infections. Authors: Mitton-Fry, M.J. / Arcari, J.T. / Brown, M.F. / Casavant, J.M. / Finegan, S.M. / Flanagan, M.E. / Gao, H. / George, D.M. / Gerstenberger, B.S. / Han, S. / Hardink, J.R. / Harris, T.M. / ...Authors: Mitton-Fry, M.J. / Arcari, J.T. / Brown, M.F. / Casavant, J.M. / Finegan, S.M. / Flanagan, M.E. / Gao, H. / George, D.M. / Gerstenberger, B.S. / Han, S. / Hardink, J.R. / Harris, T.M. / Hoang, T. / Huband, M.D. / Irvine, R. / Lall, M.S. / Megan Lemmon, M. / Li, C. / Lin, J. / McCurdy, S.P. / Mueller, J.P. / Mullins, L. / Niosi, M. / Noe, M.C. / Pattavina, D. / Penzien, J. / Plummer, M.S. / Risley, H. / Schuff, B.P. / Shanmugasundaram, V. / Starr, J.T. / Sun, J. / Winton, J. / Young, J.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4fsf.cif.gz | 204 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4fsf.ent.gz | 168.8 KB | Display | PDB format |
PDBx/mmJSON format | 4fsf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fs/4fsf ftp://data.pdbj.org/pub/pdb/validation_reports/fs/4fsf | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 58141.211 Da / Num. of mol.: 1 / Fragment: UNP residues 50-579 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: ftsI / Production host: Escherichia coli (E. coli) / References: UniProt: Q02H22, UniProt: Q51504*PLUS |
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#2: Chemical | ChemComp-0W0 / ( |
#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: 2.14 Å3/Da / Density % sol: 42.39 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 30% PEG4000, 0.2M MgCl2 0.1M Tris pH8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 1, 2010 |
Radiation | Monochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 25112 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 39.98 Å2 |
Reflection shell | Resolution: 2.2→2.28 Å / % possible all: 85.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→25.11 Å / Cor.coef. Fo:Fc: 0.9384 / Cor.coef. Fo:Fc free: 0.8976 / SU R Cruickshank DPI: 0.328 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 49.16 Å2
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Refine analyze | Luzzati coordinate error obs: 0.392 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→25.11 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.29 Å / Total num. of bins used: 13
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Refinement TLS params. | Method: refined / Origin x: 5.4564 Å / Origin y: -19.9527 Å / Origin z: -1.4919 Å
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Refinement TLS group | Selection details: { A|53 - A|563 } |