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- PDB-7fi0: Crystal structure of Multi-functional Polysaccharide lyase Smlt14... -
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Open data
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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 | |||||||||
![]() | Polysaccharide lyase | |||||||||
![]() | LYASE / Anionic Polysaccharide lyase | |||||||||
Function / homology | ![]() 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 | ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Pandey, S. / Berger, B.W. / Acharya, R. | |||||||||
Funding support | ![]() ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 82.8 KB | Display | ![]() |
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PDB format | ![]() | 57.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 790.2 KB | Display | ![]() |
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Full document | ![]() | 792.2 KB | Display | |
Data in XML | ![]() | 15.3 KB | Display | |
Data in CIF | ![]() | 21.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7fhuSC ![]() 7fhvC ![]() 7fhwC ![]() 7fhxC ![]() 7fhyC ![]() 7fhzC ![]() 7fi1C ![]() 7fi2C 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 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.) ![]() Strain: K279a / Gene: Smlt1473 / Plasmid: pET28a(+) / Production host: ![]() ![]() 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: ![]() |
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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: ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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