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- PDB-7ny3: Crystal structure of Paradendryphiella salina PL7A alginate lyase... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7ny3 | ||||||
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Title | Crystal structure of Paradendryphiella salina PL7A alginate lyase mutant Y223F in complex with tetra-mannuronic acid | ||||||
![]() | Alginate lyase (PL7) | ||||||
![]() | LYASE / complex / beta jelly roll / mutant / alginate lyase | ||||||
Function / homology | Alginate lyase 2 / Alginate lyase / Concanavalin A-like lectin/glucanase domain superfamily / lyase activity / Alginate lyase (PL7)![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Fredslund, F. / Welner, D.W. / Wilkens, C. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structure of Paradendryphiella salina PL7A alginate lyase mutant Y223F in complex with tetra-mannuronic acid Authors: Fredslund, F. / Welner, D.W. / Wilkens, C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 175.8 KB | Display | ![]() |
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PDB format | ![]() | 116.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 730.1 KB | Display | ![]() |
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Full document | ![]() | 732.5 KB | Display | |
Data in XML | ![]() | 13.1 KB | Display | |
Data in CIF | ![]() | 19.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7nczS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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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: 25452.715 Da / Num. of mol.: 1 / Mutation: Y223F Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() References: UniProt: A0A485PVH1, mannuronate-specific alginate lyase |
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#2: Polysaccharide | beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid- ...beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid Type: oligosaccharide / Mass: 1074.758 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source |
#3: Chemical | ChemComp-BTB / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.16 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: 20% PEG 1500 and 0.1 M TBG buffer pH 4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 20, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.972425 Å / Relative weight: 1 |
Reflection | Resolution: 1.81→40.47 Å / Num. obs: 39520 / % possible obs: 98.3 % / Redundancy: 6.99 % / Biso Wilson estimate: 26.52 Å2 / CC1/2: 0.99 / Net I/σ(I): 8.33 |
Reflection shell | Resolution: 1.81→1.92 Å / Num. unique obs: 5938 / CC1/2: 0.47 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7NCZ Resolution: 1.82→40.47 Å / SU ML: 0.2629 / Cross valid method: FREE R-VALUE / σ(F): 1.16 / Phase error: 22.3771 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: 30.87 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.82→40.47 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A
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