+Open data
-Basic information
Entry | Database: PDB / ID: 4bl2 | ||||||
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Title | Crystal structure of PBP2a clinical mutant E150K from MRSA | ||||||
Components | PENICILLIN BINDING PROTEIN 2 PRIME | ||||||
Keywords | HYDROLASE / PENICILLIN BINDING PROTEINS / B-LACTUM ANTIBIOTICS | ||||||
Function / homology | Function and homology information peptidoglycan L,D-transpeptidase activity / penicillin binding / cell wall organization / membrane => GO:0016020 / response to antibiotic / membrane Similarity search - Function | ||||||
Biological species | STAPHYLOCOCCUS AUREUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.72 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 | 4bl2.cif.gz | 513.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4bl2.ent.gz | 422.4 KB | Display | PDB format |
PDBx/mmJSON format | 4bl2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4bl2_validation.pdf.gz | 451.3 KB | Display | wwPDB validaton report |
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Full document | 4bl2_full_validation.pdf.gz | 467.7 KB | Display | |
Data in XML | 4bl2_validation.xml.gz | 45.8 KB | Display | |
Data in CIF | 4bl2_validation.cif.gz | 64.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bl/4bl2 ftp://data.pdbj.org/pub/pdb/validation_reports/bl/4bl2 | HTTPS FTP |
-Related structure data
Related structure data | 4bl3C 4cpkC 1vqqS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 73415.906 Da / Num. of mol.: 2 / Fragment: RESIDUES 26-668 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) STAPHYLOCOCCUS AUREUS (bacteria) / Strain: MU50 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR References: UniProt: Q54113, UniProt: A0A0H3JPA5*PLUS, serine-type D-Ala-D-Ala carboxypeptidase #2: Chemical | ChemComp-CD / #3: Chemical | ChemComp-CL / #4: 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: 53.29 % / Description: NONE |
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Crystal grow | pH: 7 / Details: pH 7 |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54179 |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54179 Å / Relative weight: 1 |
Reflection | Resolution: 2.72→19.89 Å / Num. obs: 42164 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 14.1 % / Biso Wilson estimate: 55.6 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 16.1 |
Reflection shell | Resolution: 2.72→2.87 Å / Redundancy: 11.4 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 7.5 / % possible all: 96.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1VQQ Resolution: 2.72→19.89 Å / Cor.coef. Fo:Fc: 0.9273 / Cor.coef. Fo:Fc free: 0.8577 / SU R Cruickshank DPI: 5.047 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.383 / SU Rfree Cruickshank DPI: 0.39 / Details: DISORDERED REGIONS WERE NOT MODELED
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Displacement parameters | Biso mean: 53 Å2
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Refine analyze | Luzzati coordinate error obs: 0.416 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.72→19.89 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.72→2.79 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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Refinement TLS group |
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