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- PDB-6uav: Crystal structure of a GH128 (subgroup II) endo-beta-1,3-glucanas... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6uav | ||||||
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Title | Crystal structure of a GH128 (subgroup II) endo-beta-1,3-glucanase from Pseudomonas viridiflava (PvGH128_II) | ||||||
![]() | Glyco_hydro_cc domain-containing protein | ||||||
![]() | HYDROLASE / Glycosyl hydrolase / CARBOHYDRATE | ||||||
Function / homology | Uncharacterised protein family, glycosyl hydrolase catalytic domain / Glycosyl hydrolase catalytic core / Glycoside hydrolase superfamily / Glyco_hydro_cc domain-containing protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Santos, C.R. / Costa, P.A.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 | ![]() | 120.9 KB | Display | ![]() |
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PDB format | ![]() | 93.1 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 ![]() 6uawC ![]() 6uaxC ![]() 6uayC ![]() 6uazC ![]() 6ub0C ![]() 6ub1C ![]() 6ub2C ![]() 6ub3C ![]() 6ub4C ![]() 6ub5C ![]() 6ub6C ![]() 6ub7C ![]() 6ub8C ![]() 6ubaC ![]() 6ubbC ![]() 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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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 29600.262 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||||
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#2: Chemical | #3: Chemical | ChemComp-GOL / | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.93 Å3/Da / Density % sol: 36.32 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: ammonium sulfate 2 M bis-tris 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: Jul 10, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.23986 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→43.45 Å / Num. obs: 36444 / % possible obs: 99.2 % / Redundancy: 5.38 % / CC1/2: 0.999 / Rmerge(I) obs: 0.091 / Rrim(I) all: 0.1 / Net I/σ(I): 12.19 |
Reflection shell | Resolution: 1.5→1.59 Å / Redundancy: 5.06 % / Rmerge(I) obs: 0.844 / Mean I/σ(I) obs: 1.74 / Num. unique obs: 5775 / CC1/2: 0.702 / Rrim(I) all: 0.941 / % possible all: 98.1 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.569 Å2
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Refinement step | Cycle: 1 / Resolution: 1.5→40.33 Å
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Refine LS restraints |
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