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Yorodumi- PDB-7pl3: Crystal structure of catalytic domain in closed conformation of L... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7pl3 | ||||||||||||
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Title | Crystal structure of catalytic domain in closed conformation of LytB from Streptococcus pneumoniae | ||||||||||||
Components | Putative endo-beta-N-acetylglucosaminidaseEndoglycosidase H | ||||||||||||
Keywords | HYDROLASE / glucosaminidase / peptidoglycan hydrolase | ||||||||||||
Function / homology | Function and homology information mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase / mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase activity / amidase activity / cell wall organization / extracellular region Similarity search - Function | ||||||||||||
Biological species | Streptococcus pneumoniae R6 (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||||||||
Authors | Martinez Caballero, S. / Hermoso, J.A. | ||||||||||||
Funding support | 1items
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Citation | Journal: Cell Rep / Year: 2023 Title: Molecular basis of the final step of cell division in Streptococcus pneumoniae. Authors: Martinez-Caballero, S. / Freton, C. / Molina, R. / Bartual, S.G. / Gueguen-Chaignon, V. / Mercy, C. / Gago, F. / Mahasenan, K.V. / Munoz, I.G. / Lee, M. / Hesek, D. / Mobashery, S. / ...Authors: Martinez-Caballero, S. / Freton, C. / Molina, R. / Bartual, S.G. / Gueguen-Chaignon, V. / Mercy, C. / Gago, F. / Mahasenan, K.V. / Munoz, I.G. / Lee, M. / Hesek, D. / Mobashery, S. / Hermoso, J.A. / Grangeasse, C. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7pl3.cif.gz | 134.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7pl3.ent.gz | 100.9 KB | Display | PDB format |
PDBx/mmJSON format | 7pl3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pl/7pl3 ftp://data.pdbj.org/pub/pdb/validation_reports/pl/7pl3 | HTTPS FTP |
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-Related structure data
Related structure data | 7pj3C 7pj4C 7pj5C 7pj6C 7pl2C 7pl5C 7podC 4q2wS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 30896.420 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pneumoniae R6 (bacteria) / Strain: ATCC BAA-255 / R6 / Gene: lytB, SP_0965 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P59205, mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase | ||||||
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#2: Chemical | ChemComp-1PE / | ||||||
#3: Chemical | #4: Chemical | ChemComp-CA / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.15 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: PEG 300 Bis-Tris calcium acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 8, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97926 Å / Relative weight: 1 |
Reflection | Resolution: 1.78→43.43 Å / Num. obs: 26519 / % possible obs: 99.7 % / Redundancy: 5.6 % / Biso Wilson estimate: 19.58 Å2 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.042 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 1.78→1.82 Å / Rmerge(I) obs: 0.763 / Num. unique obs: 1491 / Rpim(I) all: 0.354 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4Q2W Resolution: 1.8→43.43 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.945 / SU B: 6.695 / SU ML: 0.088 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.264 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 71.59 Å2 / Biso mean: 24.393 Å2 / Biso min: 11.56 Å2
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Refinement step | Cycle: final / Resolution: 1.8→43.43 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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