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Yorodumi- PDB-6ub6: Crystal structure of a GH128 (subgroup IV) endo-beta-1,3-glucanas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ub6 | |||||||||
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Title | Crystal structure of a GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes (LeGH128_IV) in complex with laminaritetraose | |||||||||
Components | Endo-beta-1,3-glucanase | |||||||||
Keywords | HYDROLASE / Glycosyl hydrolase / CARBOHYDRATE | |||||||||
Function / homology | fungal-type cell wall polysaccharide metabolic process / Uncharacterised protein family, glycosyl hydrolase catalytic domain / Glycosyl hydrolase catalytic core / fungal-type cell wall / Glycoside hydrolase superfamily / beta-laminaribiose / Endo-beta-1,3-glucanase Function and homology information | |||||||||
Biological species | Lentinula edodes (shiitake mushroom) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å | |||||||||
Authors | Santos, C.R. / Lima, E.A. / Mandelli, F. / Murakami, M.T. | |||||||||
Funding support | Brazil, 1items
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Citation | Journal: Nat.Chem.Biol. / Year: 2020 Title: Structural insights into beta-1,3-glucan cleavage by a glycoside hydrolase family. Authors: Santos, C.R. / Costa, P.A.C.R. / Vieira, P.S. / Gonzalez, S.E.T. / Correa, T.L.R. / Lima, E.A. / Mandelli, F. / Pirolla, R.A.S. / Domingues, M.N. / Cabral, L. / Martins, M.P. / Cordeiro, R.L. ...Authors: Santos, C.R. / Costa, P.A.C.R. / Vieira, P.S. / Gonzalez, S.E.T. / Correa, T.L.R. / Lima, E.A. / Mandelli, F. / Pirolla, R.A.S. / Domingues, M.N. / Cabral, L. / Martins, M.P. / Cordeiro, R.L. / Junior, A.T. / Souza, B.P. / Prates, E.T. / Gozzo, F.C. / Persinoti, G.F. / Skaf, M.S. / Murakami, M.T. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ub6.cif.gz | 69.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ub6.ent.gz | 52.3 KB | Display | PDB format |
PDBx/mmJSON format | 6ub6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ub/6ub6 ftp://data.pdbj.org/pub/pdb/validation_reports/ub/6ub6 | HTTPS FTP |
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-Related structure data
Related structure data | 6uaqC 6uarC 6uasC 6uatC 6uauC 6uavC 6uawC 6uaxC 6uayC 6uazC 6ub0C 6ub1C 6ub2C 6ub3C 6ub4C 6ub5C 6ub7C 6ub8C 6ubaC 6ubbC 6ubcC 6ubdC 6uflC 6ufzC 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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Unit cell |
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-Components
#1: Protein | Mass: 28780.826 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lentinula edodes (shiitake mushroom) / Gene: glu1 / Production host: Escherichia coli (E. coli) / References: UniProt: G9M5R4 |
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#2: Polysaccharide | beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#3: Polysaccharide | beta-D-glucopyranose-(1-3)-beta-D-glucopyranose / beta-laminaribiose |
#4: Chemical | ChemComp-CL / |
#5: 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: 1.87 Å3/Da / Density % sol: 34.27 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: 1.6 M ammonium sulfate 5% dioxane 0.1 M MES pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.03318 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 1, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03318 Å / Relative weight: 1 |
Reflection | Resolution: 1.25→50 Å / Num. obs: 58956 / % possible obs: 99.1 % / Redundancy: 5.9 % / CC1/2: 0.999 / Rrim(I) all: 0.109 / Net I/σ(I): 10.54 |
Reflection shell | Resolution: 1.25→1.33 Å / Redundancy: 5.6 % / Num. unique obs: 9283 / CC1/2: 0.659 / Rrim(I) all: 1.302 / % possible all: 98.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.25→49.25 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.963 / Cross valid method: FREE R-VALUE / ESU R: 0.05 / ESU R Free: 0.05 Details: HYDROGENS HAVE BEEN ADDED IN THEIR RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.5 Å2
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Refinement step | Cycle: LAST / Resolution: 1.25→49.25 Å
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