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- PDB-7fi2: Crystal structure of Multi-functional Polysaccharide lyase Smlt14... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7fi2 | |||||||||
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Title | Crystal structure of Multi-functional Polysaccharide lyase Smlt1473-H168A from Stenotrophomonas maltophilia (strain K279a) 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 | ![]() | 80.1 KB | Display | ![]() |
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PDB format | ![]() | 55.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 445.3 KB | Display | ![]() |
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Full document | ![]() | 446.4 KB | Display | |
Data in XML | ![]() | 13.7 KB | Display | |
Data in CIF | ![]() | 18.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7fhuSC ![]() 7fhvC ![]() 7fhwC ![]() 7fhxC ![]() 7fhyC ![]() 7fhzC ![]() 7fi0C ![]() 7fi1C 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
#1: Protein | Mass: 35361.633 Da / Num. of mol.: 1 / Mutation: H168A 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: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 53.03 % Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS. |
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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 trihdyrate pH-5.0 25% (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: Dec 23, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→65.44 Å / Num. obs: 11515 / % possible obs: 96.4 % / Redundancy: 10.07 % / CC1/2: 0.996 / Rmerge(I) obs: 0.114 / Net I/σ(I): 16.59 |
Reflection shell | Resolution: 2.6→2.7 Å / Redundancy: 4.25 % / Rmerge(I) obs: 0.3313 / Num. unique obs: 1013 / CC1/2: 0.909 / % possible all: 78.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7FHU Resolution: 2.6→65.309 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.891 / SU B: 9.059 / SU ML: 0.191 / Cross valid method: FREE R-VALUE / ESU R: 0.844 / ESU R Free: 0.297 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: 20.782 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→65.309 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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