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- PDB-7o79: Structure of the PL6 family polysaccharide lyase Pedsa3628 from P... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7o79 | ||||||
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Title | Structure of the PL6 family polysaccharide lyase Pedsa3628 from Pseudopedobacter saltans | ||||||
![]() | Poly(Beta-D-mannuronate) lyase | ||||||
![]() | LYASE / beta helix / polysaccharide lyase | ||||||
Function / homology | ![]() mannuronate-specific alginate lyase / poly(beta-D-mannuronate) lyase activity Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ballut, L. / Violot, S. / Carrique, L. / Aghajari, N. | ||||||
![]() | ![]() Title: Exploring molecular determinants of polysaccharide lyase family 6-1 enzyme activity. Authors: Violot, S. / Galisson, F. / Carrique, L. / Jugnarain, V. / Conchou, L. / Robert, X. / Thureau, A. / Helbert, W. / Aghajari, N. / Ballut, L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 105.8 KB | Display | ![]() |
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PDB format | ![]() | 76.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 429.3 KB | Display | ![]() |
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Full document | ![]() | 430.9 KB | Display | |
Data in XML | ![]() | 19.7 KB | Display | |
Data in CIF | ![]() | 29.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7o77C ![]() 7o78C ![]() 7o7aC ![]() 7o7tC ![]() 7o84C ![]() 6itgS 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: 49978.199 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: The first residue of the construct is not seen in the electron density Source: (gene. exp.) ![]() Strain: ATCC 51119 / DSM 12145 / JCM 21818 / LMG 10337 / NBRC 100064 / NCIMB 13643 Gene: Pedsa_3628 / Plasmid: pET28a / Production host: ![]() ![]() References: UniProt: F0S4Y3, mannuronate-specific alginate lyase |
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#2: Chemical | ChemComp-PO4 / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.58 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / Details: 0.2 M K phosphate, 20% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 19, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95372 Å / Relative weight: 1 |
Reflection | Resolution: 1.93→48.49 Å / Num. obs: 32727 / % possible obs: 98.5 % / Redundancy: 6.6 % / CC1/2: 0.996 / Net I/σ(I): 8 |
Reflection shell | Resolution: 1.93→2.05 Å / Num. unique obs: 5026 / CC1/2: 0.54 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6ITG Resolution: 1.93→48.49 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.9 / Stereochemistry target values: ML
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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 max: 64.73 Å2 / Biso mean: 29.5505 Å2 / Biso min: 15.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.93→48.49 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11
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