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Yorodumi- PDB-7fi0: Crystal structure of Multi-functional Polysaccharide lyase Smlt14... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7fi0 | |||||||||
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Title | Crystal structure of Multi-functional Polysaccharide lyase Smlt1473 (WT) from Stenotrophomonas maltophilia (strain K279a) in ManA bound form at pH-5.0 | |||||||||
Components | Polysaccharide lyase | |||||||||
Keywords | LYASE / Anionic Polysaccharide lyase | |||||||||
Function / homology | Function and homology information glucuronan lyase / glucuronan lyase activity / mannuronate-specific alginate lyase / poly(beta-D-mannuronate) lyase activity / Lyases; Carbon-oxygen lyases; Acting on polysaccharides / hyaluronate lyase / hyaluronate lyase activity / polysaccharide catabolic process / cell outer membrane / periplasmic space Similarity search - Function | |||||||||
Biological species | Stenotrophomonas maltophilia K279a (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.31 Å | |||||||||
Authors | Pandey, S. / Berger, B.W. / Acharya, R. | |||||||||
Funding support | India, United States, 2items
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Citation | Journal: J.Biol.Chem. / Year: 2021 Title: Structural insights into the mechanism of pH-selective substrate specificity of the polysaccharide lyase Smlt1473. Authors: Pandey, S. / Mahanta, P. / Berger, B.W. / Acharya, R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7fi0.cif.gz | 82.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7fi0.ent.gz | 57.9 KB | Display | PDB format |
PDBx/mmJSON format | 7fi0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fi/7fi0 ftp://data.pdbj.org/pub/pdb/validation_reports/fi/7fi0 | HTTPS FTP |
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-Related structure data
Related structure data | 7fhuSC 7fhvC 7fhwC 7fhxC 7fhyC 7fhzC 7fi1C 7fi2C 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 35428.699 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Stenotrophomonas maltophilia K279a (bacteria) Strain: K279a / Gene: Smlt1473 / Plasmid: pET28a(+) / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 References: UniProt: B2FHL8, Lyases; Carbon-oxygen lyases; Acting on polysaccharides |
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#2: Polysaccharide | beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid Source method: isolated from a genetically manipulated source |
#3: Chemical | ChemComp-PEG / |
#4: Chemical | ChemComp-SO4 / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.89 Å3/Da / Density % sol: 57.4 % / Description: rod-shaped |
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Crystal grow | Temperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 0.2M LiSo4 Monohydrate, 0.1M Sodium acetate pH-5.0, 30% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR-H / Wavelength: 1.54178 Å |
Detector | Type: BRUKER PHOTON 100 / Detector: CMOS / Date: May 13, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 2.31→29.45 Å / Num. obs: 17710 / % possible obs: 95.8 % / Redundancy: 6.39 % / CC1/2: 0.989 / Rmerge(I) obs: 0.155 / Net I/σ(I): 10.04 |
Reflection shell | Resolution: 2.31→2.41 Å / Redundancy: 2.88 % / Rmerge(I) obs: 0.5597 / Mean I/σ(I) obs: 2.14 / Num. unique obs: 1763 / CC1/2: 0.578 / % possible all: 80.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7FHU Resolution: 2.31→29.402 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.891 / Cross valid method: FREE R-VALUE / ESU R: 0.318 / ESU R Free: 0.238 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: 20.624 Å2
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Refinement step | Cycle: LAST / Resolution: 2.31→29.402 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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