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Yorodumi- PDB-5ksh: Crystal structure of penicillin-binding protein 2 from Neisseria ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ksh | ||||||
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Title | Crystal structure of penicillin-binding protein 2 from Neisseria gonorrhoeae containing an A501T mutation associated with cephalosporin resistance | ||||||
Components | Penicillin-binding protein 2 | ||||||
Keywords | BIOSYNTHETIC PROTEIN / CLASS B TRANSPEPTIDASE / 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 | Fedarovich, A. / Davies, C. | ||||||
Funding support | United States, 1items
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Citation | Journal: Biochemistry / Year: 2017 Title: Alanine 501 Mutations in Penicillin-Binding Protein 2 from Neisseria gonorrhoeae: Structure, Mechanism, and Effects on Cephalosporin Resistance and Biological Fitness. Authors: Tomberg, J. / Fedarovich, A. / Vincent, L.R. / Jerse, A.E. / Unemo, M. / Davies, C. / Nicholas, R.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ksh.cif.gz | 352.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ksh.ent.gz | 287 KB | Display | PDB format |
PDBx/mmJSON format | 5ksh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ksh_validation.pdf.gz | 470.1 KB | Display | wwPDB validaton report |
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Full document | 5ksh_full_validation.pdf.gz | 482.1 KB | Display | |
Data in XML | 5ksh_validation.xml.gz | 32.1 KB | Display | |
Data in CIF | 5ksh_validation.cif.gz | 44.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ks/5ksh ftp://data.pdbj.org/pub/pdb/validation_reports/ks/5ksh | HTTPS FTP |
-Related structure data
Related structure data | 3eqvS 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: 59024.871 Da / Num. of mol.: 2 / Mutation: A501T, F504L, A510V, A516G, P551S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neisseria gonorrhoeae (bacteria) / 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 | #3: Chemical | ChemComp-SO4 / #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: 3.85 Å3/Da / Density % sol: 68 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 8.25 Details: Grown over reservoirs containing 2.2M ammonium sulfate buffered with 100 mM Tris pH 8.25 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 19, 2011 |
Radiation | Monochromator: Si (220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→46 Å / Num. obs: 71874 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Biso Wilson estimate: 42 Å2 / Rmerge(I) obs: 0.107 / Net I/σ(I): 24.7 |
Reflection shell | Resolution: 2.4→2.44 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.988 / Mean I/σ(I) obs: 2.5 / % possible all: 97.6 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 3EQV Resolution: 2.4→44.11 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.922 / SU B: 14.524 / SU ML: 0.155 / Cross valid method: THROUGHOUT / ESU R: 0.22 / ESU R Free: 0.19 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.7 Å2
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Refinement step | Cycle: 1 / Resolution: 2.4→44.11 Å
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Refine LS restraints |
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