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Yorodumi- PDB-7pj5: Crystal structure of catalytic domain of LytB from Streptococcus ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7pj5 | ||||||
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Title | Crystal structure of catalytic domain of LytB from Streptococcus pneumoniae in complex with NAG-NAG-NAG-NAG tetrasaccharide | ||||||
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 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | ||||||
Authors | Martinez Caballero, S. / Hermoso, J.A. | ||||||
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 | 7pj5.cif.gz | 130.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7pj5.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7pj5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pj/7pj5 ftp://data.pdbj.org/pub/pdb/validation_reports/pj/7pj5 | HTTPS FTP |
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-Related structure data
Related structure data | 7pj3SC 7pj4C 7pj6C 7pl2C 7pl3C 7pl5C 7podC 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
-Protein / Sugars , 2 types, 2 molecules AAA
#1: Protein | Mass: 30896.420 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pneumoniae (strain ATCC BAA-255 / R6) (bacteria) Strain: ATCC BAA-255 / R6 / Gene: lytB, spr0867 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P59206, mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase |
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#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
-Non-polymers , 4 types, 179 molecules
#3: Chemical | ChemComp-1PE / | ||||
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#4: Chemical | #5: Chemical | ChemComp-CA / | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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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: 2.21 Å3/Da / Density % sol: 44.46 % |
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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: Dec 19, 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: 1.55→46.18 Å / Num. obs: 40276 / % possible obs: 100 % / Redundancy: 12.8 % / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.017 / Net I/σ(I): 24.5 |
Reflection shell | Resolution: 1.55→1.58 Å / Rmerge(I) obs: 0.701 / Num. unique obs: 1981 / Rpim(I) all: 0.199 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7PJ3 Resolution: 1.55→46.174 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.807 / SU ML: 0.046 / Cross valid method: FREE R-VALUE / ESU R: 0.089 / ESU R Free: 0.077 Details: Hydrogens have been added in their 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 / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.592 Å2
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Refinement step | Cycle: LAST / Resolution: 1.55→46.174 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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