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Yorodumi- PDB-6fcs: The X-ray Structure of Lytic Transglycosylase Slt inactive mutant... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6fcs | ||||||||||||
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Title | The X-ray Structure of Lytic Transglycosylase Slt inactive mutant E503Q from Pseudomonas aeruginosa in complex with NAG-NAMpentapeptide-NAG-NAMpentapeptide | ||||||||||||
Components |
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Keywords | LYASE / Lytic Transglycosylase | ||||||||||||
Function / homology | Function and homology information hydrolase activity, hydrolyzing O-glycosyl compounds / periplasmic space Similarity search - Function | ||||||||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||||||||
Authors | Batuecas, M.T. / Dominguez-Gil, T. / Hermoso, J.A. | ||||||||||||
Funding support | United States, 1items
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Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6fcs.cif.gz | 147.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6fcs.ent.gz | 111.5 KB | Display | PDB format |
PDBx/mmJSON format | 6fcs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fc/6fcs ftp://data.pdbj.org/pub/pdb/validation_reports/fc/6fcs | HTTPS FTP |
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-Related structure data
Related structure data | 5ohuSC 6fbtC 6fc4C 6fcqC 6fcrC 6fcuC 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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Unit cell |
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-Components
-Protein / Polypeptide(D) , 2 types, 2 molecules AB
#1: Protein | Mass: 70350.688 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: slt, AOY09_04369, PAMH19_2049 / Production host: Escherichia coli (E. coli) References: UniProt: A0A069QJX4, UniProt: Q9HZI6*PLUS, Lyases; Carbon-oxygen lyases; Acting on polysaccharides |
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#2: Polypeptide(D) | Mass: 532.544 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Production host: Escherichia coli (E. coli) |
-Sugars , 2 types, 2 molecules
#3: 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-2-deoxy-beta-D-glucopyranoside Source method: isolated from a genetically manipulated source |
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#4: 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)-methyl 2-acetamido-3-O-[(1R)-1-carboxyethyl]-2-deoxy-beta-D-glucopyranoside Type: oligosaccharide / Mass: 987.953 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source |
-Non-polymers , 3 types, 57 molecules
#5: Chemical | #6: Chemical | ChemComp-66N / | #7: 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: 3.11 Å3/Da / Density % sol: 60.5 % |
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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: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 10, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97926 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→144.52 Å / Num. obs: 19575 / % possible obs: 99.92 % / Redundancy: 9.9 % / Rpim(I) all: 0.092 / Net I/σ(I): 9.91 |
Reflection shell | Resolution: 2.9→3 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5OHU Resolution: 2.9→144.52 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.907 / SU B: 22.977 / SU ML: 0.381 / Cross valid method: THROUGHOUT / ESU R Free: 0.42 / 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: 74.568 Å2
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Refinement step | Cycle: 1 / Resolution: 2.9→144.52 Å
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Refine LS restraints |
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