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Yorodumi- PDB-7byx: Crystal structure of exo-beta-1,3-galactanase from Phanerochaete ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7byx | ||||||
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Title | Crystal structure of exo-beta-1,3-galactanase from Phanerochaete chrysosporium Pc1,3Gal43A E208A with beta-1,3-galactotriose | ||||||
Components | Galactan 1,3-beta-galactosidase | ||||||
Keywords | HYDROLASE / Glycoside hydrolase family 43 / exo-beta-1 / 3-galactanase / arabinogalactan degrade / complex with beta-1 / 3-galactotriose / carbohydrate binding module family 35 | ||||||
Function / homology | Function and homology information galactan 1,3-beta-galactosidase / galactan 1,3-beta-galactosidase activity / carbohydrate binding / carbohydrate metabolic process / metal ion binding Similarity search - Function | ||||||
Biological species | Phanerochaete chrysosporium (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Matsuyama, K. / Ishida, T. / Kishine, N. / Fujimoto, Z. / Igarashi, K. / Kaneko, S. | ||||||
Funding support | Japan, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2020 Title: Unique active-site and subsite features in the arabinogalactan-degrading GH43 exo-beta-1,3-galactanase from Phanerochaete chrysosporium . Authors: Matsuyama, K. / Kishine, N. / Fujimoto, Z. / Sunagawa, N. / Kotake, T. / Tsumuraya, Y. / Samejima, M. / Igarashi, K. / Kaneko, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7byx.cif.gz | 454.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7byx.ent.gz | 300.4 KB | Display | PDB format |
PDBx/mmJSON format | 7byx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7byx_validation.pdf.gz | 4.4 MB | Display | wwPDB validaton report |
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Full document | 7byx_full_validation.pdf.gz | 4.5 MB | Display | |
Data in XML | 7byx_validation.xml.gz | 74.5 KB | Display | |
Data in CIF | 7byx_validation.cif.gz | 107.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/by/7byx ftp://data.pdbj.org/pub/pdb/validation_reports/by/7byx | HTTPS FTP |
-Related structure data
Related structure data | 7bysSC 7bytC 7byvC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 45477.613 Da / Num. of mol.: 4 / Mutation: E208A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Phanerochaete chrysosporium (fungus) / Strain: K-3 / Gene: Pc1,3Gal43A / Plasmid: pPICZalphaA / Production host: Komagataella pastoris (fungus) / Strain (production host): KM71H References: UniProt: Q50KB2, galactan 1,3-beta-galactosidase |
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-Sugars , 6 types, 16 molecules
#2: Polysaccharide | alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose #3: Polysaccharide | beta-D-galactopyranose-(1-3)-beta-D-galactopyranose-(1-3)-beta-D-galactopyranose Source method: isolated from a genetically manipulated source #4: Polysaccharide | Source method: isolated from a genetically manipulated source #5: Polysaccharide | #6: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | #10: Sugar | ChemComp-NAG / | |
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-Non-polymers , 4 types, 1038 molecules
#7: Chemical | ChemComp-CA / #8: Chemical | ChemComp-ACT / #9: Chemical | ChemComp-GOL / #11: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 55.06 % / Description: bipyramidial |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 0.2 M potassium nitrate, 15 % (w/v) polyethylene glycol 6000, 20 mM sodium citrate, 5 % glycerol, 10 mM beta-1,3-galactotriose |
-Data collection
Diffraction | Mean temperature: 95 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 20, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→100 Å / Num. obs: 92497 / % possible obs: 99.1 % / Redundancy: 9.7 % / Biso Wilson estimate: 30.4 Å2 / Rsym value: 0.167 / Net I/σ(I): 17 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 2.7 / Num. unique obs: 8510 / Rsym value: 0.627 / % possible all: 92 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7BYS Resolution: 2.3→31.14 Å / SU ML: 0.2633 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.7436 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: 32.98 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→31.14 Å
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Refine LS restraints |
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LS refinement shell |
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