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Yorodumi- PDB-8rbr: Neutron structure of alginate lyase PsPL7C from Paradendryphiella... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8rbr | ||||||
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Title | Neutron structure of alginate lyase PsPL7C from Paradendryphiella salina | ||||||
Components | Alginate lyase | ||||||
Keywords | LYASE / alginate lyase / neutron structure / 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 | NEUTRON DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Meilleur, F. / Morth, J.P. / Wilkens, C. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: Neutron structure of alginate lyase PsPL7C from Paradendryphiella salina Authors: Meilleur, F. / Morth, J.P. / Wilkens, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8rbr.cif.gz | 118.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8rbr.ent.gz | 85.6 KB | Display | PDB format |
PDBx/mmJSON format | 8rbr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8rbr_validation.pdf.gz | 326 KB | Display | wwPDB validaton report |
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Full document | 8rbr_full_validation.pdf.gz | 326 KB | Display | |
Data in XML | 8rbr_validation.xml.gz | 6.4 KB | Display | |
Data in CIF | 8rbr_validation.cif.gz | 11.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rb/8rbr ftp://data.pdbj.org/pub/pdb/validation_reports/rb/8rbr | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-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: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: NEUTRON DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: 20% PEG 1500; 0.1 M TBG buffer pH 4 |
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-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: N | |||||||||
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Diffraction source | Source: SPALLATION SOURCE / Site: ORNL Spallation Neutron Source / Beamline: MANDI / Wavelength: 2-4 | |||||||||
Detector | Type: ORNL ANGER CAMERA / Detector: SCINTILLATION / Date: May 12, 2020 | |||||||||
Radiation | Protocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: neutron | |||||||||
Radiation wavelength |
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Reflection | Resolution: 1.8→27.23 Å / Num. obs: 41523 / % possible obs: 84.03 % / Redundancy: 3.2 % / Biso Wilson estimate: 13.14 Å2 / CC1/2: 0.9 / Net I/σ(I): 5.29 | |||||||||
Reflection shell | Resolution: 1.8→1.84 Å / Num. unique obs: 705 / CC1/2: 0.32 |
-Processing
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→27.23 Å / SU ML: 0.1456 / Cross valid method: FREE R-VALUE / σ(F): 0.08 / Phase error: 14.8622 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.01 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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LS refinement shell |
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