[English] 日本語
Yorodumi- PDB-8bxz: Crystal structure of Paradendryphiella salina PL7C alginate lyase... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8bxz | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Paradendryphiella salina PL7C alginate lyase mutant Y220F in complex with penta-mannuronic acid | ||||||
Components | Alginate lyase | ||||||
Keywords | LYASE / beta-jeely roll / alginate lyase / mannuronate | ||||||
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: 1.2 Å | ||||||
Authors | Wilkens, C. | ||||||
Funding support | Denmark, 1items
| ||||||
Citation | Journal: To Be Published Title: Crystal structure of Paradendryphiella salina PL7C alginate lyase mutant Y220F in complex with penta-mannuronic acid Authors: Wilkens, C. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8bxz.cif.gz | 198.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8bxz.ent.gz | 131.4 KB | Display | PDB format |
PDBx/mmJSON format | 8bxz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bx/8bxz ftp://data.pdbj.org/pub/pdb/validation_reports/bx/8bxz | HTTPS FTP |
---|
-Related structure data
Related structure data | |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-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 |
---|---|
#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 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 |
---|
-Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40.16 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9762 Å |
Detector | Type: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Feb 6, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→36.62 Å / Num. obs: 58658 / % possible obs: 92.1 % / Redundancy: 3.29 % / Biso Wilson estimate: 7.16 Å2 / CC1/2: 0.99 / Net I/σ(I): 12.54 |
Reflection shell | Resolution: 1.2→1.27 Å / Num. unique obs: 9001 / CC1/2: 0.87 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→36.62 Å / SU ML: 0.0736 / Cross valid method: FREE R-VALUE / σ(F): 1.95 / Phase error: 12.5952 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.06 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.2→36.62 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|