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- PDB-6fcu: The X-ray Structure of Lytic Transglycosylase Slt inactive mutant... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6fcu | |||||||||
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Title | The X-ray Structure of Lytic Transglycosylase Slt inactive mutant E503Q from Pseudomonas aeruginosa in complex with 4(NAG-NAMpentapeptide) | |||||||||
![]() | Soluble lytic murein transglycosylase | |||||||||
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Function / homology | ![]() hydrolase activity, hydrolyzing O-glycosyl compounds / ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Batuecas, M.T. / Dominguez-Gil, T. / Hermoso, J.A. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Exolytic and endolytic turnover of peptidoglycan by lytic transglycosylase Slt ofPseudomonas aeruginosa. Authors: Lee, M. / Batuecas, M.T. / Tomoshige, S. / Dominguez-Gil, T. / Mahasenan, K.V. / Dik, D.A. / Hesek, D. / Millan, C. / Uson, I. / Lastochkin, E. / Hermoso, J.A. / Mobashery, S. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 145.8 KB | Display | ![]() |
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PDB format | ![]() | 110.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5ohuSC ![]() 6fbtC ![]() 6fc4C ![]() 6fcqC ![]() 6fcrC ![]() 6fcsC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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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: 70350.688 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() References: UniProt: A0A069QJX4, UniProt: Q9HZI6*PLUS, ![]() |
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#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-3-O-[(2R)-1-amino-1-oxopropan-2-yl]-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-3-O-[(2R)-1-amino-1-oxopropan-2-yl]-2-deoxy-beta-D-glucopyranose-(1-4)-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)-N-acetyl-beta-muramic acid-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-methyl 2-acetamido-2-deoxy-beta-D-glucopyranoside Type: oligosaccharide ![]() Source method: isolated from a genetically manipulated source |
-Non-polymers , 4 types, 56 molecules ![](data/chem/img/ACT.gif)
![](data/chem/img/ALA.gif)
![](data/chem/img/DGL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ALA.gif)
![](data/chem/img/DGL.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ![]() #4: Chemical | ChemComp-ALA / | ![]() #5: Chemical | ChemComp-DGL / | ![]() #6: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.01 Å3/Da / Density % sol: 59.14 % |
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Crystal grow![]() | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 80mM Tris pH 8.5, 12% PEG 8000 and 160mM calcium acetate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 24, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 3.2→142.28 Å / Num. obs: 14530 / % possible obs: 99.91 % / Redundancy: 9.4 % / Rpim(I) all: 0.061 / Net I/σ(I): 9.35 |
Reflection shell | Resolution: 3.2→3.32 Å |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 5OHU Resolution: 3.2→142.28 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.893 / SU B: 29.105 / SU ML: 0.454 / Cross valid method: THROUGHOUT / ESU R Free: 0.542 / 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: 94.973 Å2
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Refinement step | Cycle: 1 / Resolution: 3.2→142.28 Å
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Refine LS restraints |
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