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Yorodumi- PDB-8rtz: The structure of E. coli penicillin binding protein 3 (PBP3) in c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8rtz | ||||||||||||
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Title | The structure of E. coli penicillin binding protein 3 (PBP3) in complex with a bicyclic peptide inhibitor | ||||||||||||
Components |
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Keywords | HYDROLASE / Inhibitor / Complex / PBP3 (penicillin binding protein 3) / bicyclic peptide / transpeptidase / peptidoglycan | ||||||||||||
Function / homology | Function and homology information divisome complex / peptidoglycan glycosyltransferase activity / serine-type D-Ala-D-Ala carboxypeptidase / FtsZ-dependent cytokinesis / serine-type D-Ala-D-Ala carboxypeptidase activity / division septum assembly / cell division site / penicillin binding / peptidoglycan biosynthetic process / cell wall organization ...divisome complex / peptidoglycan glycosyltransferase activity / serine-type D-Ala-D-Ala carboxypeptidase / FtsZ-dependent cytokinesis / serine-type D-Ala-D-Ala carboxypeptidase activity / division septum assembly / cell division site / penicillin binding / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / response to xenobiotic stimulus / cell division / proteolysis / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Escherichia coli (E. coli) synthetic construct (others) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 Å | ||||||||||||
Authors | Newman, H. / Rowland, C.E. / Dods, R. / Lewis, N. / Stanway, S.J. / Bellini, D. / Beswick, P. | ||||||||||||
Funding support | United Kingdom, 3items
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Citation | Journal: To Be Published Title: Discovery and chemical optimisation of a Potent, Bi-cyclic (Bicycle) Antimicrobial Inhibitor of Escherichia coli PBP3 Authors: Rowland, C.E. / Newman, H. / Martin, T.T. / Dods, R. / Bournakas, N. / Wagstaff, J.M. / Lewis, N. / Stanway, S.J. / Blamforth, M. / Kessler, C. / van Rietschoten, K. / Bellini, D. / Roper, D. ...Authors: Rowland, C.E. / Newman, H. / Martin, T.T. / Dods, R. / Bournakas, N. / Wagstaff, J.M. / Lewis, N. / Stanway, S.J. / Blamforth, M. / Kessler, C. / van Rietschoten, K. / Bellini, D. / Roper, D.I. / Lloyd, A.J. / Dowson, C.G. / Skynner, M.J. / Beswick, P. / Dawson, M. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8rtz.cif.gz | 90.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8rtz.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8rtz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rt/8rtz ftp://data.pdbj.org/pub/pdb/validation_reports/rt/8rtz | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 37129.418 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ftsI, pbpB, b0084, JW0082 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P0AD68, serine-type D-Ala-D-Ala carboxypeptidase |
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#2: Protein/peptide | Mass: 1496.774 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: Bicyclic peptide with a scaffold covalently linking three cysteine residues. C-terminus is capped with an amine. Source: (synth.) synthetic construct (others) |
#3: Chemical | ChemComp-29N / |
#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: 2.11 Å3/Da / Density % sol: 42.9 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 0.1M Tris pH 9.0 and 20% (w/v) PEG 6K supplemented with an additive, 30% (w/v) dextran sulphate sodium salt, Mr 5K Temp details: Crystallised on ice |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 23, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.52→45.04 Å / Num. obs: 50525 / % possible obs: 99.6 % / Redundancy: 12.2 % / CC1/2: 1 / Χ2: 1.01 / Net I/av σ(I): 23.8 / Net I/σ(I): 23.8 |
Reflection shell | Resolution: 1.52→1.55 Å / Redundancy: 7.1 % / Num. unique obs: 2315 / CC1/2: 0.749 / % possible all: 93 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.52→45.04 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.015 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.078 / ESU R Free: 0.081 Details: Hydrogens have been added in their 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 / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.42 Å2
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Refinement step | Cycle: LAST / Resolution: 1.52→45.04 Å
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Refine LS restraints |
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LS refinement shell |
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