[English] 日本語
![](img/lk-miru.gif)
- PDB-6ubc: Crystal structure of a GH128 (subgroup VII) oligosaccharide-bindi... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6ubc | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of a GH128 (subgroup VII) oligosaccharide-binding protein from Cryptococcus neoformans (CnGH128_VII) | ||||||
![]() | 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. / Souza, B.P. / Vieira, P.S. / Murakami, M.T. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 69.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 52.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 415.9 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 416 KB | Display | |
Data in XML | ![]() | 13.8 KB | Display | |
Data in CIF | ![]() | 21 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 ![]() 6ubbC ![]() 6ubdC ![]() 6uflC ![]() 6ufzC C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-
Components
#1: Protein | Mass: 46711.031 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 1.48 Å3/Da / Density % sol: 16.9 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: Sodium acetate 0.1 M ammonium sulfate 2.0 M |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 18, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→48.39 Å / Num. obs: 33192 / % possible obs: 99.8 % / Redundancy: 40.1 % / CC1/2: 0.999 / Net I/σ(I): 16.65 |
Reflection shell | Resolution: 1.65→1.75 Å / Num. unique obs: 5316 / CC1/2: 0.589 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 75.3 Å2 / Biso mean: 27.362 Å2 / Biso min: 19.98 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.65→48.39 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.651→1.694 Å / Total num. of bins used: 20
|