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- PDB-7pod: Crystal structure of catalytic domain of LytB (E585Q) from Strept... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7pod | ||||||
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Title | Crystal structure of catalytic domain of LytB (E585Q) from Streptococcus pneumoniae in complex with NAG-NAM-NAG-NAM tetrasaccharide | ||||||
![]() | Putative endo-beta-N-acetylglucosaminidase | ||||||
![]() | HYDROLASE / glucosaminidase / peptidoglycan hydrolase | ||||||
Function / homology | ![]() mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase / mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase activity / amidase activity / bacterial-type flagellum-dependent cell motility / cell wall organization / extracellular region Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Martinez Caballero, S. / Hermoso, J.A. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 133 KB | Display | ![]() |
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PDB format | ![]() | 97.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 516.2 KB | Display | ![]() |
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Full document | ![]() | 519.1 KB | Display | |
Data in XML | ![]() | 8.2 KB | Display | |
Data in CIF | ![]() | 12.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7pj3C ![]() 7pj4C ![]() 7pj5C ![]() 7pj6C ![]() 7pl2C ![]() 7pl3SC ![]() 7pl5C S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 30896.420 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC BAA-255 / R6 / Gene: lytB, spr0867 / Production host: ![]() ![]() References: UniProt: P59206, mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase |
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#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-N-acetyl-beta-muramic acid-(1-4)-2-acetamido-2-deoxy- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-N-acetyl-beta-muramic acid-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-methyl 2-acetamido-3-O-[(1R)-1-carboxyethyl]-2-deoxy-beta-D-glucopyranoside Type: oligosaccharide / Mass: 988.937 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-Non-polymers , 4 types, 175 molecules ![](data/chem/img/1PE.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-1PE / |
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#4: Chemical | ChemComp-PEG / |
#5: Chemical | ChemComp-CA / |
#6: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.05 % |
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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: ![]() ![]() ![]() |
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: 1.5→46.26 Å / Num. obs: 43792 / % possible obs: 99.5 % / Redundancy: 9.9 % / Biso Wilson estimate: 18.52 Å2 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.016 / Net I/σ(I): 24 |
Reflection shell | Resolution: 1.5→1.53 Å / Rmerge(I) obs: 0.66 / Num. unique obs: 2156 / Rpim(I) all: 0.217 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7PL3 Resolution: 1.5→46.254 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.962 / SU B: 2.89 / SU ML: 0.048 / Cross valid method: FREE R-VALUE / ESU R: 0.081 / ESU R Free: 0.073 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: 22.101 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→46.254 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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