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- PDB-6ubb: Crystal structure of a GH128 (subgroup VI) exo-beta-1,3-glucanase... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ubb | |||||||||
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Title | Crystal structure of a GH128 (subgroup VI) exo-beta-1,3-glucanase from Aureobasidium namibiae (AnGH128_VI) with laminaribiose at the surface-binding site | |||||||||
![]() | Glyco_hydro_cc domain-containing protein | |||||||||
![]() | 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 / Asl1-like glycosyl hydrolase catalytic domain-containing protein![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Santos, C.R. / Vieira, P.S. / Domingues, M.N. / Cordeiro, R.L. / Tomazini, A. / Murakami, M.T. | |||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 501.9 KB | Display | ![]() |
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PDB format | ![]() | 413.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3.2 MB | Display | ![]() |
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Full document | ![]() | 3.2 MB | Display | |
Data in XML | ![]() | 85 KB | Display | |
Data in CIF | ![]() | 115 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6uaqC ![]() 6uarC ![]() 6uasC ![]() 6uatC ![]() 6uauC ![]() 6uavC ![]() 6uawC ![]() 6uaxC ![]() 6uayC ![]() 6uazC ![]() 6ub0C ![]() 6ub1C ![]() 6ub2C ![]() 6ub3C ![]() 6ub4C ![]() 6ub5C ![]() 6ub6C ![]() 6ub7C ![]() 6ub8C ![]() 6ubaC ![]() 6ubcC ![]() 6ubdC ![]() 6uflC ![]() 6ufzC C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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10 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 30811.098 Da / Num. of mol.: 10 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: M436DRAFT_66913 / Production host: ![]() ![]() #2: Polysaccharide | beta-D-glucopyranose-(1-3)-beta-D-glucopyranose / beta-laminaribiose #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.64 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 0.18 M tri-ammonium citrate, 18% v/v PEG 3,350, 0.01 M Cobalt (II) chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jun 12, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.45857 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→50 Å / Num. obs: 130821 / % possible obs: 99.9 % / Redundancy: 6.7 % / CC1/2: 0.98 / Net I/σ(I): 4.8 |
Reflection shell | Resolution: 2.35→2.49 Å / Num. unique obs: 20840 / CC1/2: 0.433 |
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Processing
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Refinement | Method to determine structure: ![]() 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: 33.87 Å2
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Refinement step | Cycle: LAST / Resolution: 2.35→49.3 Å
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Refine LS restraints |
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