[English] 日本語
Yorodumi- 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) | ||||||
Components | Glyco_hydro_cc domain-containing protein | ||||||
Keywords | 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 Function and homology information | ||||||
Biological species | Cryptococcus neoformans (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Santos, C.R. / Costa, P.A.C.R. / Souza, B.P. / Vieira, P.S. / Murakami, M.T. | ||||||
Funding support | Brazil, 1items
| ||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6ubc.cif.gz | 69.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6ubc.ent.gz | 52.1 KB | Display | PDB format |
PDBx/mmJSON format | 6ubc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ubc_validation.pdf.gz | 415.9 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6ubc_full_validation.pdf.gz | 416 KB | Display | |
Data in XML | 6ubc_validation.xml.gz | 13.8 KB | Display | |
Data in CIF | 6ubc_validation.cif.gz | 21 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ub/6ubc ftp://data.pdbj.org/pub/pdb/validation_reports/ub/6ubc | 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 (ref.) |
---|---|
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.) Cryptococcus neoformans (fungus) / Production host: Escherichia coli (E. coli) / References: UniProt: J9VNP7 |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-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: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å |
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: MOLECULAR REPLACEMENT / Resolution: 1.65→48.39 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.959 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.09 / ESU R Free: 0.093 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
|