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Yorodumi- PDB-6vbc: Crystal structure of transpeptidase domain of PBP2 from Neisseria... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6vbc | ||||||
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Title | Crystal structure of transpeptidase domain of PBP2 from Neisseria gonorrhoeae cephalosporin-resistant strain H041 | ||||||
Components | Probable peptidoglycan D,D-transpeptidase PenA | ||||||
Keywords | HYDROLASE / PENICILLIN-BINDING PROTEIN / ANTIBIOTIC RESISTANCE / TRANSPEPTIDASE DOMAIN | ||||||
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: 1.55 Å | ||||||
Authors | Singh, A. / Davies, C. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2020 Title: Mutations in Neisseria gonorrhoeae penicillin-binding protein 2 associated with extended-spectrum cephalosporin resistance create an energetic barrier against acylation via restriction of protein dynamics Authors: Singh, A. / Turner, J. / Tomberg, J. / Fedarovich, A. / Unemo, 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 | 6vbc.cif.gz | 79 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6vbc.ent.gz | 57 KB | Display | PDB format |
PDBx/mmJSON format | 6vbc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vb/6vbc ftp://data.pdbj.org/pub/pdb/validation_reports/vb/6vbc | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 35361.496 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neisseria gonorrhoeae (bacteria) / Gene: penA / Plasmid: pMAlC2KV / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: F2Z7K9, serine-type D-Ala-D-Ala carboxypeptidase |
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#2: 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: 2.41 Å3/Da / Density % sol: 49.06 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 9.3 / Details: 40% PEG 600, 0.1 M CHES |
-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: Jul 1, 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: 1.55→31.69 Å / Num. obs: 48525 / % possible obs: 98.3 % / Redundancy: 6.8 % / CC1/2: 0.994 / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.047 / Net I/σ(I): 31.8 |
Reflection shell | Resolution: 1.55→1.58 Å / Rmerge(I) obs: 0.625 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 2372 / CC1/2: 0.851 / Rpim(I) all: 0.268 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.55→31.69 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.247 / SU ML: 0.046 / Cross valid method: THROUGHOUT / ESU R: 0.078 / ESU R Free: 0.076 / 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: 17.308 Å2
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Refinement step | Cycle: 1 / Resolution: 1.55→31.69 Å
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Refine LS restraints |
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