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Yorodumi- PDB-7kcv: Crystal structure of S. aureus penicillin-binding protein 4 (PBP4... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7kcv | ||||||
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Title | Crystal structure of S. aureus penicillin-binding protein 4 (PBP4) mutant (R200L) | ||||||
Components | Penicillin-binding protein 4 | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information serine-type D-Ala-D-Ala carboxypeptidase activity / beta-lactam antibiotic catabolic process / peptidoglycan biosynthetic process / cell wall organization / beta-lactamase activity / regulation of cell shape / response to antibiotic / proteolysis / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å | ||||||
Authors | Alexander, J.A.N. / Strynadka, N.C.J. | ||||||
Funding support | Canada, 1items
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Citation | Journal: J.Antimicrob.Chemother. / Year: 2021 Title: PBP4-mediated beta-lactam resistance among clinical strains of Staphylococcus aureus. Authors: Satishkumar, N. / Alexander, J.A.N. / Poon, R. / Buggeln, E. / Argudin, M.A. / Strynadka, N.C.J. / Chatterjee, S.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7kcv.cif.gz | 271.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7kcv.ent.gz | 181.5 KB | Display | PDB format |
PDBx/mmJSON format | 7kcv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kc/7kcv ftp://data.pdbj.org/pub/pdb/validation_reports/kc/7kcv | HTTPS FTP |
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-Related structure data
Related structure data | 7kcwC 7kcxC 7kcyC 6c39S S: Starting model for refinement C: citing same article (ref.) |
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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: 41054.312 Da / Num. of mol.: 1 / Mutation: R200L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (strain COL) (bacteria) Strain: COL / Gene: pbp4, SACOL0699 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H2WY27 |
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#2: Chemical | ChemComp-ZN / |
#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: 2.63 Å3/Da / Density % sol: 53.16 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 12% PEG 6000; 100 mM sodium acetate, pH 5; and 10 mM zinc chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1.5212 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 30, 2020 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5212 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.6→45.16 Å / Num. obs: 57721 / % possible obs: 99.7 % / Redundancy: 6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.022 / Rrim(I) all: 0.055 / Net I/σ(I): 17.5 / Num. measured all: 348189 / Scaling rejects: 10 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6c39 Resolution: 1.6→42.81 Å / SU ML: 0.2024 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 21.2424 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: 32.35 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→42.81 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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