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- PDB-7fhz: Crystal structure of Multi-functional Polysaccharide lyase Smlt14... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7fhz | |||||||||
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Title | Crystal structure of Multi-functional Polysaccharide lyase Smlt1473 (WT) from Stenotrophomonas maltophilia (strain K279a) in apo form at pH 9.0 | |||||||||
![]() | 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 | ![]() | 87.6 KB | Display | ![]() |
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PDB format | ![]() | 52.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7fhuSC ![]() 7fhvC ![]() 7fhwC ![]() 7fhxC ![]() 7fhyC ![]() 7fi0C ![]() 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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1 |
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Unit cell |
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Components
#1: Protein | Mass: 34442.637 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: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 53.15 % Description: rod-shaped 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: 9 Details: 0.2 Ammonium Sulfate, 0.1M Tris-HCl, pH 9.0, 30% (w/v) PEG 4000 |
-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: Feb 28, 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: 2.45→41.19 Å / Num. obs: 13694 / % possible obs: 97.4 % / Redundancy: 6.94 % / Biso Wilson estimate: 12.11 Å2 / CC1/2: 0.971 / Rmerge(I) obs: 0.1368 / Net I/σ(I): 10.52 |
Reflection shell | Resolution: 2.45→2.55 Å / Redundancy: 1.69 % / Rmerge(I) obs: 0.3897 / Mean I/σ(I) obs: 1.87 / Num. unique obs: 1338 / CC1/2: 0.545 / % possible all: 86.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7FHU Resolution: 2.5→35.73 Å / SU ML: 0.3791 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.6686 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.73 Å2 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→35.73 Å
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Refine LS restraints |
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LS refinement shell |
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