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Yorodumi- PDB-4oon: Crystal structure of PBP1a in complex with compound 17 ((4Z,8S,11... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4oon | ||||||
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Title | Crystal structure of PBP1a in complex with compound 17 ((4Z,8S,11E,14S)-5-(2-amino-1,3-thiazol-4-yl)-14-(5,6-dihydroxy-1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl)-8-formyl-2-methyl-6-oxo-3,10-dioxa-4,7,11-triazatetradeca-4,11-diene-2,12,14-tricarboxylic acid) | ||||||
Components | Penicillin-binding protein 1A | ||||||
Keywords | transferase/transferase inhibitor / PBP1A / transferase-transferase inhibitor complex | ||||||
Function / homology | Function and homology information : / peptidoglycan glycosyltransferase / peptidoglycan glycosyltransferase activity / serine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / penicillin binding / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / membrane => GO:0016020 ...: / peptidoglycan glycosyltransferase / peptidoglycan glycosyltransferase activity / serine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / penicillin binding / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / membrane => GO:0016020 / response to antibiotic / plasma membrane Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa PAO1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||
Authors | Han, S. / Caspers, N. / Knafels, J.D. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2014 Title: Siderophore receptor-mediated uptake of lactivicin analogues in gram-negative bacteria. Authors: Starr, J. / Brown, M.F. / Aschenbrenner, L. / Caspers, N. / Che, Y. / Gerstenberger, B.S. / Huband, M. / Knafels, J.D. / Lemmon, M.M. / Li, C. / McCurdy, S.P. / McElroy, E. / Rauckhorst, M.R. ...Authors: Starr, J. / Brown, M.F. / Aschenbrenner, L. / Caspers, N. / Che, Y. / Gerstenberger, B.S. / Huband, M. / Knafels, J.D. / Lemmon, M.M. / Li, C. / McCurdy, S.P. / McElroy, E. / Rauckhorst, M.R. / Tomaras, A.P. / Young, J.A. / Zaniewski, R.P. / Shanmugasundaram, V. / Han, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4oon.cif.gz | 217.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4oon.ent.gz | 170.5 KB | Display | PDB format |
PDBx/mmJSON format | 4oon.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oo/4oon ftp://data.pdbj.org/pub/pdb/validation_reports/oo/4oon | HTTPS FTP |
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-Related 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: 88379.742 Da / Num. of mol.: 1 / Fragment: PBP1A: unp residues 36-822 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: mrcA, ponA, PA5045 / Production host: Escherichia coli (E. coli) References: UniProt: Q07806, Transferases; Glycosyltransferases; Pentosyltransferases, Hydrolases; Acting on peptide bonds (peptidases) |
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#2: Chemical | ChemComp-2U4 / ( |
#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: 2.26 Å3/Da / Density % sol: 45.58 % |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 5.6 Details: 0.1M sodium citrate pH 5.6, 1.2M ammonium phosphate, VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 173 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 18, 2012 |
Radiation | Monochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→100 Å / Num. all: 175377 / Num. obs: 13985 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 93.05 Å2 |
Reflection shell | Resolution: 3.199→3.21 Å / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→27.72 Å / Cor.coef. Fo:Fc: 0.9338 / Cor.coef. Fo:Fc free: 0.9034 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 82.04 Å2
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Refine analyze | Luzzati coordinate error obs: 0.555 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.2→27.72 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.2→3.46 Å / Total num. of bins used: 7
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Refinement TLS params. | Method: refined / Origin x: -27.8957 Å / Origin y: 25.2953 Å / Origin z: 1.187 Å
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Refinement TLS group | Selection details: { A|* } |