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- PDB-6ub3: Crystal structure of a GH128 (subgroup IV) endo-beta-1,3-glucanas... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ub3 | |||||||||
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Title | Crystal structure of a GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes (LeGH128_IV) with laminaribiose at the surface-binding site | |||||||||
![]() | glycoside hydrolase![]() | |||||||||
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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![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Santos, C.R. / Lima, E.A. / Mandelli, F. / 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 | ![]() | 209.1 KB | Display | ![]() |
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PDB format | ![]() | 165 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6uaqC ![]() 6uarC ![]() 6uasC ![]() 6uatC ![]() 6uauC ![]() 6uavC ![]() 6uawC ![]() 6uaxC ![]() 6uayC ![]() 6uazC ![]() 6ub0C ![]() 6ub1C ![]() 6ub2SC ![]() 6ub4C ![]() 6ub5C ![]() 6ub6C ![]() 6ub7C ![]() 6ub8C ![]() 6ubaC ![]() 6ubbC ![]() 6ubcC ![]() 6ubdC ![]() 6uflC ![]() 6ufzC S: Starting model for refinement 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein / Sugars , 2 types, 4 molecules AB
#1: Protein | ![]() Mass: 28780.826 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #2: Polysaccharide | |
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-Non-polymers , 4 types, 531 molecules ![](data/chem/img/CL.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ![]() #4: Chemical | ChemComp-MES / | ![]() #5: Chemical | ![]() #6: Water | ChemComp-HOH / | ![]() |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.47 Å3/Da / Density % sol: 64.6 % |
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Crystal grow![]() | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: ammonium sulfate 1.5 M 10% dioxane MMT 0.1 M |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 12, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.85→44.18 Å / Num. obs: 60216 / % possible obs: 96.2 % / Redundancy: 6.44 % / CC1/2: 0.999 / Net I/σ(I): 13.45 |
Reflection shell | Resolution: 1.85→1.96 Å / Num. unique obs: 9698 / CC1/2: 0.847 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 6UB2 Resolution: 1.85→44.18 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.953 / SU B: 6.94 / SU ML: 0.101 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.11 / ESU R Free: 0.11 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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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 max: 90.68 Å2 / Biso mean: 32.694 Å2 / Biso min: 21.97 Å2
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Refinement step | Cycle: final / Resolution: 1.85→44.18 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.851→1.899 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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