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Yorodumi- PDB-8c5o: Crystal Structure of Penicillin-binding Protein 3 (PBP3) from Sta... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8c5o | ||||||
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Title | Crystal Structure of Penicillin-binding Protein 3 (PBP3) from Staphylococcus Epidermidis in complex with Vaborbactam | ||||||
Components | Penicillin-binding protein 3 | ||||||
Keywords | PENICILLIN-BINDING PROTEIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Staphylococcus epidermidis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Schwinzer, M. / Brognaro, H. / Rohde, H. / Betzel, C. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Int J Appl Biol Pharm / Year: 2023 Title: Structure and Dynamics of the Penicillin-Binding Protein 3 from Staphylococcus Epidermidis Native and in Complex with Cefotaxime and Vaborbactam Authors: Schwinzer, M. / Brognaro, H. / Rohde, H. / Betzel, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8c5o.cif.gz | 170.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8c5o.ent.gz | 110.5 KB | Display | PDB format |
PDBx/mmJSON format | 8c5o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c5/8c5o ftp://data.pdbj.org/pub/pdb/validation_reports/c5/8c5o | HTTPS FTP |
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-Related structure data
Related structure data | 8c5bC 8c5wC 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
#1: Protein | Mass: 74932.000 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus epidermidis (strain ATCC 35984 / RP62A) Gene: pbp3, SERP1117 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5HNZ7 |
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#2: Chemical | ChemComp-4D6 / |
#3: 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: 3.53 Å3/Da / Density % sol: 65.17 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: Ammonium sulfate + Vaborbactam |
-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: 0.82655 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 24, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.82655 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→80.245 Å / Num. obs: 50577 / % possible obs: 92.6 % / Redundancy: 18.2 % / Biso Wilson estimate: 36.29 Å2 / CC1/2: 0.9642 / Net I/σ(I): 3.988 |
Reflection shell | Resolution: 2.309→2.364 Å / Num. unique obs: 3160 / CC1/2: 0.9642 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→50.95 Å / SU ML: 0.2548 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.1967 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→50.95 Å
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Refine LS restraints |
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LS refinement shell |
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