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Yorodumi- PDB-6fbt: The X-ray Structure of Lytic Transglycosylase Slt from Pseudomona... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6fbt | ||||||||||||
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Title | The X-ray Structure of Lytic Transglycosylase Slt from Pseudomonas aeruginosa in complex with the reaction product NAG-anhNAMpentapeptide | ||||||||||||
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: 2.5 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 | 6fbt.cif.gz | 144.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6fbt.ent.gz | 109.9 KB | Display | PDB format |
PDBx/mmJSON format | 6fbt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6fbt_validation.pdf.gz | 802.8 KB | Display | wwPDB validaton report |
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Full document | 6fbt_full_validation.pdf.gz | 809.3 KB | Display | |
Data in XML | 6fbt_validation.xml.gz | 24.7 KB | Display | |
Data in CIF | 6fbt_validation.cif.gz | 34.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fb/6fbt ftp://data.pdbj.org/pub/pdb/validation_reports/fb/6fbt | HTTPS FTP |
-Related structure data
Related structure data | 5ohuSC 6fc4C 6fcqC 6fcrC 6fcsC 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) / Sugars , 3 types, 3 molecules AE
#1: Protein | Mass: 69974.328 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: PA3020 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HZI6 |
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#2: Polypeptide(D) | Mass: 532.544 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Pseudomonas aeruginosa (bacteria) |
#4: Sugar | ChemComp-NAG / |
-Non-polymers , 3 types, 101 molecules
#3: Chemical | ChemComp-PO4 / #5: Chemical | ChemComp-AH0 / | #6: 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: 3.05 Å3/Da / Density % sol: 59.67 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 1.4M sodium potassium phosphate pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97919 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 19, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97919 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→143.35 Å / Num. obs: 30002 / % possible obs: 99.93 % / Redundancy: 15.2 % / Rpim(I) all: 0.024 / Net I/σ(I): 15.2 |
Reflection shell | Resolution: 2.5→2.59 Å / Rpim(I) all: 0.36 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5OHU Resolution: 2.5→143.35 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.933 / SU B: 11.323 / SU ML: 0.234 / Cross valid method: THROUGHOUT / ESU R: 0.371 / ESU R Free: 0.259 / 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: 67.247 Å2
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Refinement step | Cycle: 1 / Resolution: 2.5→143.35 Å
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Refine LS restraints |
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