+Open data
-Basic information
Entry | Database: PDB / ID: 4bl3 | ||||||
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Title | Crystal structure of PBP2a clinical mutant N146K from MRSA | ||||||
Components | PENICILLIN BINDING PROTEIN 2 PRIME | ||||||
Keywords | HYDROLASE / MRSA / ALLOSTERIC SITE / B-LACTAM ANTIBIOTICS | ||||||
Function / homology | Function and homology information penicillin binding / membrane => GO:0016020 / response to antibiotic / membrane Similarity search - Function | ||||||
Biological species | STAPHYLOCOCCUS AUREUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Otero, L.H. / Rojas-Altuve, A. / Carrasco-Lopez, C. / 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 | 4bl3.cif.gz | 525.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4bl3.ent.gz | 434.3 KB | Display | PDB format |
PDBx/mmJSON format | 4bl3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bl/4bl3 ftp://data.pdbj.org/pub/pdb/validation_reports/bl/4bl3 | HTTPS FTP |
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-Related structure data
Related structure data | 4bl2C 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: 73143.641 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: 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: 2.68 Å3/Da / Density % sol: 54.07 % / 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: 3→69.07 Å / Num. obs: 30067 / % possible obs: 83.2 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Biso Wilson estimate: 70.72 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 8.3 |
Reflection shell | Resolution: 3→3.16 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 1.9 / % possible all: 75.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1VQQ Resolution: 3→48.74 Å / Cor.coef. Fo:Fc: 0.9066 / Cor.coef. Fo:Fc free: 0.8571 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.6 Details: DISORDERED REGIONS WERE NOT MODELED. IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=CD CL. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=10421. NUMBER ...Details: DISORDERED REGIONS WERE NOT MODELED. IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=CD CL. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=10421. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=4. NUMBER TREATED BY BAD NON-BONDED CONTACTS=7.
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Displacement parameters | Biso mean: 75.68 Å2
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Refine analyze | Luzzati coordinate error obs: 0.543 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→48.74 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.12 Å / Total num. of bins used: 13
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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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