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Yorodumi- PDB-8bjo: Crystal structure of Paradendryphiella salina PL7C alginate lyase... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8bjo | ||||||
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Title | Crystal structure of Paradendryphiella salina PL7C alginate lyase mutant Y220F in complex with hexa-mannuronic acid | ||||||
Components | Alginate lyase | ||||||
Keywords | LYASE / beta-jelly roll / alginate lyase / complex | ||||||
Function / homology | Alginate lyase 2 / Alginate lyase / Concanavalin A-like lectin/glucanase domain superfamily / lyase activity / Alginate lyase Function and homology information | ||||||
Biological species | Paradendryphiella salina (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 Å | ||||||
Authors | Wilkens, C. / Morth, J.P. | ||||||
Funding support | Denmark, 1items
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Citation | Journal: To Be Published Title: Crystal structure of Paradendryphiella salina PL7C alginate lyase mutant Y220F in complex with hexa-mannuronic acid Authors: Wilkens, C. / Morth, J.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8bjo.cif.gz | 173 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8bjo.ent.gz | 112.8 KB | Display | PDB format |
PDBx/mmJSON format | 8bjo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8bjo_validation.pdf.gz | 606.6 KB | Display | wwPDB validaton report |
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Full document | 8bjo_full_validation.pdf.gz | 608.8 KB | Display | |
Data in XML | 8bjo_validation.xml.gz | 13.1 KB | Display | |
Data in CIF | 8bjo_validation.cif.gz | 19.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bj/8bjo ftp://data.pdbj.org/pub/pdb/validation_reports/bj/8bjo | HTTPS FTP |
-Related structure data
Related structure data | 6ywfS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 25528.244 Da / Num. of mol.: 1 / Mutation: Y220F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Paradendryphiella salina (fungus) / Gene: PsAlg7C / Production host: Komagataella pastoris (fungus) / References: UniProt: A0A7I9C8Z1 |
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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-SO4 / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 39.13 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 2 M Ammonium sulfate; 0.1 Sodium acetate pH 4.6 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.7749 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 2, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.7749 Å / Relative weight: 1 |
Reflection | Resolution: 1.51→19.05 Å / Num. obs: 28650 / % possible obs: 91.08 % / Redundancy: 3.8 % / Biso Wilson estimate: 13.2 Å2 / CC1/2: 1 / Net I/σ(I): 8.35 |
Reflection shell | Resolution: 1.51→1.56 Å / Num. unique obs: 2660 / CC1/2: 0.86 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6YWF Resolution: 1.51→19.05 Å / SU ML: 0.156 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 24.1936 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: 17.74 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.51→19.05 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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