+Open data
-Basic information
Entry | Database: PDB / ID: 7ony | ||||||
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Title | Crystal structure of PBP3 from P. aeruginosa | ||||||
Components | Peptidoglycan D,D-transpeptidase FtsI | ||||||
Keywords | MEMBRANE PROTEIN / PBP3 / peptidoglycan synthesis | ||||||
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 / 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 / molecular replacement / Resolution: 1.77 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 | 7ony.cif.gz | 246 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ony.ent.gz | 174 KB | Display | PDB format |
PDBx/mmJSON format | 7ony.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/on/7ony ftp://data.pdbj.org/pub/pdb/validation_reports/on/7ony | HTTPS FTP |
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-Related structure data
Related structure data | 7onkC 7onnC 7onoC 7onwC 7onxC 7onzC 3oc2S 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 57615.797 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria) Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 Gene: ftsI, pbpB, PA4418 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: G3XD46, serine-type D-Ala-D-Ala carboxypeptidase | ||||||||
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#2: Chemical | ChemComp-GOL / #3: Chemical | #4: Chemical | ChemComp-DMS / | #5: 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: 3.53 Å3/Da / Density % sol: 65.19 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 9 mg/ml PBP3, 0.1 M MES, 5% (w/v) PEG3000; 30% (v/v) PEG200, 10% DMSO |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9999 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 10, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9999 Å / Relative weight: 1 |
Reflection | Resolution: 1.77→39.55 Å / Num. obs: 42918 / % possible obs: 70.4 % / Redundancy: 7 % / CC1/2: 0.998 / Rrim(I) all: 0.07 / Net I/σ(I): 13.9 |
Reflection shell | Resolution: 1.773→1.966 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2146 / CC1/2: 0.641 / Rrim(I) all: 1.159 / % possible all: 4.4 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3OC2 Resolution: 1.77→39.55 Å / SU ML: 0.2149 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 31.3493 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: 49.99 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.77→39.55 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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