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Yorodumi- PDB-8c0m: Crystal structure of Paradendryphiella salina PL7C alginate lyase... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8c0m | ||||||
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Title | Crystal structure of Paradendryphiella salina PL7C alginate lyase mutant Y220F | ||||||
Components | Alginate lyase | ||||||
Keywords | LYASE / beta-jelly roll / alginate lyase | ||||||
Function / homology | Alginate lyase 2 / Alginate lyase / Concanavalin A-like lectin/glucanase domain superfamily / lyase activity / ACETATE ION / Alginate lyase Function and homology information | ||||||
Biological species | Paradendryphiella salina (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å | ||||||
Authors | Wilkens, C. | ||||||
Funding support | Denmark, 1items
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Citation | Journal: To Be Published Title: Crystal structure of Paradendryphiella salina PL7C alginate lyase mutant Y220F Authors: Wilkens, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8c0m.cif.gz | 185.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8c0m.ent.gz | 122.6 KB | Display | PDB format |
PDBx/mmJSON format | 8c0m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c0/8c0m ftp://data.pdbj.org/pub/pdb/validation_reports/c0/8c0m | 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: 25528.244 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: Chemical | ChemComp-ACT / | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 39.33 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / 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: 0.9786 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 5, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→20.31 Å / Num. obs: 57526 / % possible obs: 91.28 % / Redundancy: 3.5 % / Biso Wilson estimate: 10.17 Å2 / CC1/2: 0.99 / Net I/σ(I): 9.31 |
Reflection shell | Resolution: 1.2→1.24 Å / Num. unique obs: 4767 / CC1/2: 0.75 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→20.31 Å / SU ML: 0.0928 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 18.7197 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: 15.62 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.2→20.31 Å
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Refine LS restraints |
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LS refinement shell |
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