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Yorodumi- PDB-6p54: Crystal structure of transpeptidase domain of PBP2 from Neisseria... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6p54 | ||||||
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Title | Crystal structure of transpeptidase domain of PBP2 from Neisseria gonorrhoeae acylated by ceftriaxone | ||||||
Components | Probable peptidoglycan D,D-transpeptidase PenA | ||||||
Keywords | HYDROLASE/ANTIBIOTIC / Penicillin-binding protein / transpeptidase domain / Neisseria gonorrhoeae / antibiotic resistance / HYDROLASE-ANTIBIOTIC complex | ||||||
Function / homology | Function and homology information peptidoglycan glycosyltransferase activity / serine-type D-Ala-D-Ala carboxypeptidase / FtsZ-dependent cytokinesis / division septum assembly / serine-type D-Ala-D-Ala carboxypeptidase activity / 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 / division septum assembly / serine-type D-Ala-D-Ala carboxypeptidase activity / 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: 1.83 Å | ||||||
Authors | Singh, A. / Davies, C. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2019 Title: Recognition of the beta-lactam carboxylate triggers acylation ofNeisseria gonorrhoeaepenicillin-binding protein 2. Authors: Singh, A. / Tomberg, J. / 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 | 6p54.cif.gz | 139.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6p54.ent.gz | 113.3 KB | Display | PDB format |
PDBx/mmJSON format | 6p54.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p5/6p54 ftp://data.pdbj.org/pub/pdb/validation_reports/p5/6p54 | HTTPS FTP |
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-Related 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 35326.262 Da / Num. of mol.: 2 / Fragment: UNP residues 237-574 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neisseria gonorrhoeae (bacteria) / Gene: penA / Plasmid: pMAL-C2KV / Production host: Escherichia coli (E. coli) / Strain (production host): GW6011 References: UniProt: P08149, serine-type D-Ala-D-Ala carboxypeptidase |
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-Non-polymers , 5 types, 214 molecules
#2: Chemical | ChemComp-NZV / |
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#3: Chemical | ChemComp-CEF / |
#4: Chemical | ChemComp-9F2 / |
#5: Chemical | ChemComp-PEG / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.6 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9.3 / Details: 0.1 M CHES, 40% PEG600 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 7, 2019 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.83→35.01 Å / Num. obs: 50936 / % possible obs: 98.8 % / Redundancy: 5.2 % / Biso Wilson estimate: 25.9 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.041 / Net I/σ(I): 29.1 |
Reflection shell | Resolution: 1.83→1.86 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.643 / Mean I/σ(I) obs: 2 / Num. unique obs: 2469 / CC1/2: 0.801 / Rpim(I) all: 0.335 / % possible all: 97.2 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.83→35.01 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.961 / SU B: 3.74 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.143 / ESU R Free: 0.13 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 33.9 Å2
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Refinement step | Cycle: 1 / Resolution: 1.83→35.01 Å
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Refine LS restraints |
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