+Open data
-Basic information
Entry | Database: PDB / ID: 7ono | ||||||
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Title | Crystal structure of PBP3 transpeptidase domain from E. coli | ||||||
Components | Peptidoglycan D,D-transpeptidase FtsI | ||||||
Keywords | MEMBRANE PROTEIN / PBP3 / peptidoglycan synthesis / transpeptidase domain | ||||||
Function / homology | Function and homology information divisome complex / peptidoglycan glycosyltransferase activity / serine-type D-Ala-D-Ala carboxypeptidase / FtsZ-dependent cytokinesis / division septum assembly / serine-type D-Ala-D-Ala carboxypeptidase activity / 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 / division septum assembly / serine-type D-Ala-D-Ala carboxypeptidase activity / 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) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å | ||||||
Authors | Freischem, S. / Grimm, I. / Weiergraeber, O.H. | ||||||
Citation | Journal: Biomolecules / Year: 2021 Title: Interaction Mode of the Novel Monobactam AIC499 Targeting Penicillin Binding Protein 3 of Gram-Negative Bacteria. Authors: Freischem, S. / Grimm, I. / Lopez-Perez, A. / Willbold, D. / Klenke, B. / Vuong, C. / Dingley, A.J. / Weiergraber, O.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ono.cif.gz | 188.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ono.ent.gz | 133.9 KB | Display | PDB format |
PDBx/mmJSON format | 7ono.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ono_validation.pdf.gz | 250.5 KB | Display | wwPDB validaton report |
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Full document | 7ono_full_validation.pdf.gz | 252.7 KB | Display | |
Data in XML | 7ono_validation.xml.gz | 9.3 KB | Display | |
Data in CIF | 7ono_validation.cif.gz | 13.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/on/7ono ftp://data.pdbj.org/pub/pdb/validation_reports/on/7ono | HTTPS FTP |
-Related structure data
Related structure data | 7onkC 7onnC 7onwC 7onxC 7onyC 7onzC 4bjpS 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: 43696.766 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / 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: Chemical | ChemComp-TMO / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.84 Å3/Da / Density % sol: 56.76 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 14.4 mg/ml PBP3, 0.1 M sodium cacodylate, 5% (w/v) PEG 8000, 20% (v/v) MPD, 0.2% (w/v) betaine, 0.2% (w/v) L-glutamic acid, 0.2% (w/v) L-proline, 0.2% (w/v) taurine, 0.2% (w/v) trimethlyamin ...Details: 14.4 mg/ml PBP3, 0.1 M sodium cacodylate, 5% (w/v) PEG 8000, 20% (v/v) MPD, 0.2% (w/v) betaine, 0.2% (w/v) L-glutamic acid, 0.2% (w/v) L-proline, 0.2% (w/v) taurine, 0.2% (w/v) trimethlyamin N-oxide, 0.02 M HEPES |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 4, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 2.298→47.743 Å / Num. obs: 9457 / % possible obs: 93.9 % / Redundancy: 17.8 % / CC1/2: 0.999 / Rrim(I) all: 0.103 / Net I/σ(I): 20.7 |
Reflection shell | Resolution: 2.298→2.603 Å / Redundancy: 15.7 % / Mean I/σ(I) obs: 2.4 / Num. unique obs: 473 / CC1/2: 0.84 / Rrim(I) all: 1.456 / % possible all: 74.6 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4BJP Resolution: 2.3→47.74 Å / SU ML: 0.2205 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.4743 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 66.52 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→47.74 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A
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