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Yorodumi- PDB-6p53: Crystal structure of the transpeptidase domain of PBP2 from Neiss... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6p53 | ||||||
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Title | Crystal structure of the transpeptidase domain of PBP2 from Neisseria gonorrhoeae in apo form | ||||||
Components | peptidoglycan D,D-transpeptidase PenA | ||||||
Keywords | HYDROLASE / Penicillin-binding protein / transpeptidase domain / N. gonorrhoeae / antibiotic resistance | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.92 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 | 6p53.cif.gz | 139.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6p53.ent.gz | 107.1 KB | Display | PDB format |
PDBx/mmJSON format | 6p53.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6p53_validation.pdf.gz | 282.8 KB | Display | wwPDB validaton report |
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Full document | 6p53_full_validation.pdf.gz | 282.8 KB | Display | |
Data in XML | 6p53_validation.xml.gz | 1.1 KB | Display | |
Data in CIF | 6p53_validation.cif.gz | 8.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p5/6p53 ftp://data.pdbj.org/pub/pdb/validation_reports/p5/6p53 | HTTPS FTP |
-Related structure data
Related structure data | 6p52C 6p54C 6p55C 6p56C 4u3tS S: Starting model for refinement C: citing same article (ref.) |
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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: 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 #2: Chemical | ChemComp-PO4 / | #3: 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: 2.18 Å3/Da / Density % sol: 43.6 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9.3 / Details: 40% PEG600, 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: Feb 20, 2018 |
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: 1.92→36.09 Å / Num. obs: 42141 / % possible obs: 90.8 % / Redundancy: 6.3 % / Biso Wilson estimate: 26 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.022 / Net I/σ(I): 33.9 |
Reflection shell | Resolution: 1.92→1.95 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.413 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 2272 / CC1/2: 0.93 / Rpim(I) all: 0.191 / % possible all: 97.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4U3T Resolution: 1.92→36.09 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.941 / SU B: 3.982 / SU ML: 0.115 / Cross valid method: THROUGHOUT / ESU R: 0.187 / ESU R Free: 0.165 / 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: 33.881 Å2
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Refinement step | Cycle: 1 / Resolution: 1.92→36.09 Å
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Refine LS restraints |
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