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Yorodumi- PDB-8c5b: Crystal Structure of Penicillin-binding Protein 3 (PBP3) from Sta... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8c5b | ||||||
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Title | Crystal Structure of Penicillin-binding Protein 3 (PBP3) from Staphylococcus Epidermidis | ||||||
Components | Penicillin-binding protein 3 | ||||||
Keywords | PENICILLIN-BINDING PROTEIN | ||||||
Function / homology | Penicillin-binding protein, dimerisation domain / Penicillin-binding Protein dimerisation domain / Penicillin-binding protein, dimerisation domain superfamily / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / penicillin binding / Beta-lactamase/transpeptidase-like / membrane / Penicillin-binding protein 3 Function and homology information | ||||||
Biological species | Staphylococcus epidermidis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 | 8c5b.cif.gz | 304.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8c5b.ent.gz | 205.3 KB | Display | PDB format |
PDBx/mmJSON format | 8c5b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c5/8c5b ftp://data.pdbj.org/pub/pdb/validation_reports/c5/8c5b | HTTPS FTP |
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-Related structure data
Related structure data | 8c5oC 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) (bacteria) Gene: pbp3, SERP1117 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5HNZ7 |
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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: 3.57 Å3/Da / Density % sol: 65.52 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: Ammonium sulfate |
-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: 0.97625 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: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 2.067→80.687 Å / Num. obs: 46353 / % possible obs: 95.2 % / Redundancy: 18.8 % / Biso Wilson estimate: 56.24 Å2 / CC1/2: 0.999 / Net I/σ(I): 16.8 |
Reflection shell | Resolution: 2.067→2.297 Å / Num. unique obs: 2318 / CC1/2: 0.996 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→57.94 Å / SU ML: 0.3166 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.7949 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: 71.95 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→57.94 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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