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Yorodumi- PDB-4cpk: Crystal structure of PBP2a double clinical mutant N146K-E150K fro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4cpk | ||||||
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Title | Crystal structure of PBP2a double clinical mutant N146K-E150K from MRSA | ||||||
Components | Penicillin binding protein 2 prime | ||||||
Keywords | HYDROLASE / PENICILLIN-BINDING PROTEIN / MRSA / ALLOSTERIC SITE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | ||||||
Authors | Otero, L.H. / Rojas-Altuve, A. / Hermoso, J.A. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2014 Title: Disruption of Allosteric Response as an Unprecedented Mechanism of Resistance to Antibiotics. Authors: Fishovitz, J. / Rojas-Altuve, A. / Otero, L.H. / Dawley, M. / Carrasco-Lopez, C. / Chang, M. / Hermoso, J.A. / Mobashery, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4cpk.cif.gz | 538.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4cpk.ent.gz | 441.5 KB | Display | PDB format |
PDBx/mmJSON format | 4cpk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cp/4cpk ftp://data.pdbj.org/pub/pdb/validation_reports/cp/4cpk | HTTPS FTP |
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-Related structure data
Related structure data | 4bl2C 4bl3C 3zg0S 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 73430.984 Da / Num. of mol.: 2 / Fragment: RESIDUES 26-668 / Mutation: YES,N146K,E150K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (strain Mu50 / ATCC 700699) (bacteria) Strain: Mu50 / ATCC 700699 / Gene: mecA, SAV0041 / Plasmid: pET24D / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR / References: UniProt: A0A0H3JPA5 #2: Chemical | ChemComp-CD / #3: Chemical | ChemComp-CL / #4: Sugar | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 53.28 % / Description: NONE |
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Crystal grow | pH: 7 / Details: pH 7 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8729 |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8729 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→46.64 Å / Num. obs: 65572 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 8.3 % / Biso Wilson estimate: 40.68 Å2 / Rmerge(I) obs: 0.16 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 2.35→2.48 Å / Redundancy: 8.4 % / Rmerge(I) obs: 0.94 / Mean I/σ(I) obs: 2.3 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3ZG0 Resolution: 2.35→46.64 Å / Cor.coef. Fo:Fc: 0.9387 / Cor.coef. Fo:Fc free: 0.9077 / SU R Cruickshank DPI: 0.306 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.33 / SU Rfree Blow DPI: 0.225 / SU Rfree Cruickshank DPI: 0.222
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Displacement parameters | Biso mean: 47.43 Å2
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Refine analyze | Luzzati coordinate error obs: 0.306 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.35→46.64 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.35→2.41 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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