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Yorodumi- PDB-7pbf: Crystal structure of Paradendryphiella salina PL7A alginate lyase... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7pbf | ||||||
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Title | Crystal structure of Paradendryphiella salina PL7A alginate lyase in complex with di-mannuronic acid | ||||||
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: 1.54 Å | ||||||
Authors | Fredslund, F. / Welner, D.H. / Wilkens, C. | ||||||
Funding support | European Union, 1items
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Citation | Journal: To Be Published Title: Crystal structure of Paradendryphiella salina PL7A alginate lyase in complex with di-mannuronic acid Authors: Fredslund, F. / Welner, D.H. / Wilkens, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7pbf.cif.gz | 172.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7pbf.ent.gz | 113.9 KB | Display | PDB format |
PDBx/mmJSON format | 7pbf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7pbf_validation.pdf.gz | 873.4 KB | Display | wwPDB validaton report |
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Full document | 7pbf_full_validation.pdf.gz | 873.6 KB | Display | |
Data in XML | 7pbf_validation.xml.gz | 11.4 KB | Display | |
Data in CIF | 7pbf_validation.cif.gz | 15.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pb/7pbf ftp://data.pdbj.org/pub/pdb/validation_reports/pb/7pbf | HTTPS FTP |
-Related structure data
Related structure data | 7nczS 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: 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 |
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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: 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: 2.25 Å3/Da / Density % sol: 45.32 % |
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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 |
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Diffraction source | Source: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.976254 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 24, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976254 Å / Relative weight: 1 |
Reflection | Resolution: 1.54→40.32 Å / Num. obs: 34390 / % possible obs: 99.5 % / Redundancy: 12.89 % / Biso Wilson estimate: 25.9 Å2 / CC1/2: 1 / Net I/σ(I): 18.68 |
Reflection shell | Resolution: 1.54→1.64 Å / Num. unique obs: 5324 / CC1/2: 0.65 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7NCZ Resolution: 1.54→40.32 Å / SU ML: 0.2054 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.1641 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: 35.41 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.54→40.32 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
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