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Yorodumi- PDB-8pdt: Crystal structure of Paradendryphiella salina PL7C alginate lyase... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8pdt | ||||||
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Title | Crystal structure of Paradendryphiella salina PL7C alginate lyase soaked with dimannuronic acid | ||||||
Components | Alginate lyase | ||||||
Keywords | LYASE / Alginate lyase / complex / beta-jelly roll | ||||||
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: 1.09 Å | ||||||
Authors | Wilknes, C. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: Crystal structure of Paradendryphiella salina PL7C alginate lyase soaked with dimannuronic acid Authors: Wilknes, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8pdt.cif.gz | 195.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8pdt.ent.gz | 129.7 KB | Display | PDB format |
PDBx/mmJSON format | 8pdt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pd/8pdt ftp://data.pdbj.org/pub/pdb/validation_reports/pd/8pdt | HTTPS FTP |
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-Related structure data
Related structure data | |
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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: 25544.244 Da / Num. of mol.: 1 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)-alpha-D-mannopyranuronic acid Source method: isolated from a genetically manipulated source |
#3: Polysaccharide | beta-D-mannopyranuronic acid-(1-4)-alpha-L-gulopyranuronic acid Source method: isolated from a genetically manipulated source |
#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: 2.18 Å3/Da / Density % sol: 43.45 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 30% PEG3350, 0.1M Bis-Tris pH 5.5, 0.3M NaCl |
-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: 0.799 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 22, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.799 Å / Relative weight: 1 |
Reflection | Resolution: 1.09→44.88 Å / Num. obs: 92201 / % possible obs: 98.4 % / Redundancy: 7.16 % / Biso Wilson estimate: 13.33 Å2 / CC1/2: 1 / Net I/σ(I): 7.77 |
Reflection shell | Resolution: 1.09→1.16 Å / Num. unique obs: 14459 / CC1/2: 0.46 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.09→37.77 Å / SU ML: 0.1232 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.71 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: 18.07 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.09→37.77 Å
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Refine LS restraints |
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LS refinement shell |
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