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Yorodumi- PDB-3eqv: Crystal structure of penicillin-binding protein 2 from Neisseria ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3eqv | ||||||
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Title | Crystal structure of penicillin-binding protein 2 from Neisseria gonorrhoeae containing four mutations associated with penicillin resistance | ||||||
Components | Penicillin-binding protein 2 | ||||||
Keywords | BIOSYNTHETIC PROTEIN / Penicillin-binding protein / Class B transpeptidase / penicillin resistance / Cell division / Cell inner membrane / Cell membrane / Cell shape / Cell wall biogenesis/degradation / Peptidoglycan synthesis | ||||||
Function / homology | Function and homology information peptidoglycan glycosyltransferase activity / serine-type D-Ala-D-Ala carboxypeptidase / FtsZ-dependent cytokinesis / serine-type D-Ala-D-Ala carboxypeptidase activity / division septum assembly / penicillin binding / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / response to antibiotic ...peptidoglycan glycosyltransferase activity / serine-type D-Ala-D-Ala carboxypeptidase / FtsZ-dependent cytokinesis / serine-type D-Ala-D-Ala carboxypeptidase activity / division septum assembly / penicillin binding / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / response to antibiotic / proteolysis / plasma membrane Similarity search - Function | ||||||
Biological species | Neisseria gonorrhoeae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.4 Å | ||||||
Authors | Powell, A.J. / Deacon, A.M. / Nicholas, R.A. / Davies, C. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2009 Title: Crystal Structures of Penicillin-binding Protein 2 from Penicillin-susceptible and -resistant Strains of Neisseria gonorrhoeae Reveal an Unexpectedly Subtle Mechanism for Antibiotic Resistance. Authors: Powell, A.J. / Tomberg, J. / Deacon, A.M. / Nicholas, R.A. / Davies, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3eqv.cif.gz | 179.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3eqv.ent.gz | 140.3 KB | Display | PDB format |
PDBx/mmJSON format | 3eqv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3eqv_validation.pdf.gz | 475.9 KB | Display | wwPDB validaton report |
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Full document | 3eqv_full_validation.pdf.gz | 487.4 KB | Display | |
Data in XML | 3eqv_validation.xml.gz | 32.3 KB | Display | |
Data in CIF | 3eqv_validation.cif.gz | 44.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eq/3eqv ftp://data.pdbj.org/pub/pdb/validation_reports/eq/3eqv | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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5 |
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Unit cell |
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-Components
#1: Protein | Mass: 59108.957 Da / Num. of mol.: 2 / Mutation: F504L, A510V, A516G, P551S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neisseria gonorrhoeae (bacteria) / Strain: 6140 / Gene: penA / Plasmid: pMAL-C2KV/H6 / Production host: Escherichia coli (E. coli) / Strain (production host): GW6011 References: UniProt: P08149, serine-type D-Ala-D-Ala carboxypeptidase #2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Water | ChemComp-HOH / | |
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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: 3.84 Å3/Da / Density % sol: 67.97 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 2.2 M ammonium sulphate, 100 mM Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97934 Å |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Nov 11, 2006 |
Radiation | Monochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. all: 71399 / Num. obs: 71399 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 49.1 Å2 / Rsym value: 0.101 / Net I/σ(I): 29.9 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 2.7 / Num. unique all: 5957 / Rsym value: 0.52 / % possible all: 83.5 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: Wild-type structure Resolution: 2.4→48.1 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.921 / SU B: 15.651 / SU ML: 0.171 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.219 / ESU R Free: 0.197 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.7 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→48.1 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.454 Å / Total num. of bins used: 20
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