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Yorodumi- PDB-8vbu: Structure of the monofunctional Staphylococcus aureus PBP1 in its... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8vbu | ||||||
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Title | Structure of the monofunctional Staphylococcus aureus PBP1 in its beta-lactam (Oxacillin) inhibited form | ||||||
Components | Penicillin-binding protein 1 | ||||||
Keywords | HYDROLASE/INHIBITOR / ANTIBIOTIC / Penicillin Binding Protein 1 / Peptidoglycan Transpeptidase domain / Pedestal domain / MEMBRANE PROTEIN / HYDROLASE-INHIBITOR / ANTIBIOTIC complex | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Staphylococcaceae bacterium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Bon, C.G. / Lee, J. / Caveney, N.A. / Strynadka, N.C.J. | ||||||
Funding support | Canada, 1items
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Citation | Journal: J.Struct.Biol. / Year: 2024 Title: Structural and kinetic analysis of the monofunctional Staphylococcus aureus PBP1. Authors: Bon, C.G. / Grigg, J.C. / Lee, J. / Robb, C.S. / Caveney, N.A. / Eltis, L.D. / Strynadka, N.C.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8vbu.cif.gz | 412.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8vbu.ent.gz | 332.5 KB | Display | PDB format |
PDBx/mmJSON format | 8vbu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vb/8vbu ftp://data.pdbj.org/pub/pdb/validation_reports/vb/8vbu | HTTPS FTP |
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-Related structure data
Related structure data | 8vbtC 8vbvC 8vbwC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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: 66644.258 Da / Num. of mol.: 2 / Fragment: residues 39-608 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcaceae bacterium (bacteria) / Gene: SAOUHSC_01145 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: Q2FZ94 #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 39.49 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / Details: 0.18M ammonium citrate 22% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03321 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 26, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03321 Å / Relative weight: 1 |
Reflection | Resolution: 2→87.55 Å / Num. obs: 73247 / % possible obs: 99.3 % / Redundancy: 2.8 % / CC1/2: 0.726 / Rmerge(I) obs: 0.276 / Rpim(I) all: 0.257 / Net I/σ(I): 3.8 |
Reflection shell | Resolution: 2→2.04 Å / Redundancy: 2.9 % / Rmerge(I) obs: 1.452 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4466 / CC1/2: 0.339 / Rpim(I) all: 1.337 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→54.97 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 23.23 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→54.97 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 |
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