[English] 日本語
Yorodumi- PDB-7p90: Crystal structure of Paradendryphiella salina PL7A alginate lyase... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7p90 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Paradendryphiella salina PL7A alginate lyase in complex with tetra-mannuronic acid products | ||||||
Components | Alginate lyase (PL7) | ||||||
Keywords | 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) Function and homology information | ||||||
Biological species | Paradendryphiella salina (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å | ||||||
Authors | Fredslund, F. / Welner, D.H. / Wilkens, C. | ||||||
Funding support | Denmark, 1items
| ||||||
Citation | Journal: To Be Published Title: Crystal structure of Paradendryphiella salina PL7A alginate lyase in complex with tetra-mannuronic acid products Authors: Fredslund, F. / Welner, D.H. / Wilkens, C. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7p90.cif.gz | 174.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7p90.ent.gz | 115.5 KB | Display | PDB format |
PDBx/mmJSON format | 7p90.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7p90_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7p90_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7p90_validation.xml.gz | 12.7 KB | Display | |
Data in CIF | 7p90_validation.cif.gz | 17.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p9/7p90 ftp://data.pdbj.org/pub/pdb/validation_reports/p9/7p90 | HTTPS FTP |
-Related structure data
Related structure data | 7nczS S: Starting model for refinement |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 25468.715 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Paradendryphiella salina (fungus) / Gene: PsAlg7A / Production host: Komagataella pastoris (fungus) / References: UniProt: A0A485PVH1 |
---|---|
#2: Polysaccharide | 4-deoxy-alpha-L-erythro-hex-4-enopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid-(1-4)-beta-D- ...4-deoxy-alpha-L-erythro-hex-4-enopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid Type: oligosaccharide / Mass: 528.372 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source |
#3: Polysaccharide | beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic 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 |
---|
-Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 45.99 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.953798 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: 0.953798 Å / Relative weight: 1 |
Reflection | Resolution: 1.87→40.46 Å / Num. obs: 19676 / % possible obs: 98.4 % / Redundancy: 12.72 % / Biso Wilson estimate: 35.25 Å2 / CC1/2: 1 / Net I/σ(I): 24.74 |
Reflection shell | Resolution: 1.87→1.98 Å / Num. unique obs: 2869 / CC1/2: 0.94 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7NCZ Resolution: 1.87→36.41 Å / SU ML: 0.2074 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 24.9231 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: 46.52 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.87→36.41 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A
|