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Yorodumi- PDB-4ool: Crystal structure of PBP3 in complex with compound 14 ((2E)-2-({[... -
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-Basic information
Entry | Database: PDB / ID: 4ool | ||||||
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Title | Crystal structure of PBP3 in complex with compound 14 ((2E)-2-({[(2S)-2-{[(2Z)-2-(2-amino-1,3-thiazol-4-yl)-2-{[(1,5-dihydroxy-4-oxo-1,4-dihydropyridin-2-yl)methoxy]imino}acetyl]amino}-3-oxopropyl]oxy}imino)pentanedioic acid) | ||||||
Components | Cell division protein FtsI [Peptidoglycan synthetase] | ||||||
Keywords | transferase/transferase inhibitor / PBP3 / transferase-transferase inhibitor complex | ||||||
Function / homology | Beta-Lactamase - #330 / Beta-Lactamase / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta / Chem-2U2 / : Function and homology information | ||||||
Biological species | Pseudomonas aeruginosa PA1R (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 | 4ool.cif.gz | 209.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ool.ent.gz | 167 KB | Display | PDB format |
PDBx/mmJSON format | 4ool.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ool_validation.pdf.gz | 770.1 KB | Display | wwPDB validaton report |
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Full document | 4ool_full_validation.pdf.gz | 778.8 KB | Display | |
Data in XML | 4ool_validation.xml.gz | 20.9 KB | Display | |
Data in CIF | 4ool_validation.cif.gz | 29.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oo/4ool ftp://data.pdbj.org/pub/pdb/validation_reports/oo/4ool | HTTPS FTP |
-Related structure data
Related structure data | 4oomC 4oonC 3pbnS 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: 58329.453 Da / Num. of mol.: 1 / Fragment: penicillin binding protein, unp residues 50-579 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa PA1R (bacteria) / Gene: PA1R_gp2318 / Production host: Escherichia coli (E. coli) References: UniProt: U6AVY0, peptidoglycan glycosyltransferase |
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#2: Chemical | ChemComp-2U2 / ( |
#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: 2.18 Å3/Da / Density % sol: 43.63 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 30% PEG 4K, 0.2M MgCl2, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
-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: 2.3→100 Å / Num. all: 142397 / Num. obs: 23399 / % possible obs: 98.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 60.21 Å2 / Rmerge(I) obs: 0.045 |
Reflection shell | Resolution: 2.287→2.294 Å / Rmerge(I) obs: 0.491 / Mean I/σ(I) obs: 2.2 / % possible all: 77.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 3PBN Resolution: 2.3→27.27 Å / Cor.coef. Fo:Fc: 0.9441 / Cor.coef. Fo:Fc free: 0.9198 / SU R Cruickshank DPI: 0.313 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 70.86 Å2
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Refine analyze | Luzzati coordinate error obs: 0.351 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→27.27 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.29→2.39 Å / Total num. of bins used: 12
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Refinement TLS params. | Method: refined / Origin x: 28.9717 Å / Origin y: 20.8355 Å / Origin z: -1.1898 Å
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Refinement TLS group | Selection details: { A|53 - A|561 } |