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- PDB-6kzk: Structure of alginate lyase Aly36B mutant K143A/M171A in complex ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6kzk | ||||||
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Title | Structure of alginate lyase Aly36B mutant K143A/M171A in complex with alginate trisaccharide | ||||||
![]() | Alginate lyase | ||||||
![]() | LYASE | ||||||
Function / homology | : / Polysaccharide lyase 14 / Prokaryotic membrane lipoprotein lipid attachment site profile. / metal ion binding / Uncharacterized protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhang, Y.Z. / Dong, F. / Chen, X.L. | ||||||
![]() | ![]() Title: Alginate Lyase Aly36B is a New Bacterial Member of the Polysaccharide Lyase Family 36 and Catalyzes by a Novel Mechanism With Lysine as Both the Catalytic Base and Catalytic Acid. Authors: Dong, F. / Xu, F. / Chen, X.L. / Li, P.Y. / Li, C.Y. / Li, F.C. / Chen, Y. / Wang, P. / Zhang, Y.Z. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 157.3 KB | Display | ![]() |
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PDB format | ![]() | 124.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 29.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 26487.859 Da / Num. of mol.: 3 / Mutation: K109A, M137A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.85 Å3/Da / Density % sol: 56.91 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: potassium phosphate dibasic, PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 1, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2.789→50 Å / Num. obs: 21758 / % possible obs: 97.2 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.183 / Net I/σ(I): 15.2 |
Reflection shell | Resolution: 2.789→2.85 Å / Rmerge(I) obs: 0.395 / Num. unique obs: 1088 |
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Processing
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Refinement | Method to determine structure: ![]()
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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: 63.64 Å2 / Biso mean: 22.7457 Å2 / Biso min: 4.29 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.789→40.842 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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