[English] 日本語
Yorodumi- PDB-6ub7: Crystal structure of a GH128 (subgroup V) exo-beta-1,3-glucanase ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ub7 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of a GH128 (subgroup V) exo-beta-1,3-glucanase from Cryptococcus neoformans (CnGH128_V) | ||||||
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: 1.8 Å | ||||||
Authors | Santos, C.R. / Costa, P.A.C.R. / 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 | 6ub7.cif.gz | 69.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6ub7.ent.gz | 49.5 KB | Display | PDB format |
PDBx/mmJSON format | 6ub7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ub/6ub7 ftp://data.pdbj.org/pub/pdb/validation_reports/ub/6ub7 | 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 6ub8C 6ubaC 6ubbC 6ubcC 6ubdC 6uflC 6ufzC C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 32774.156 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: J9VQQ4 |
---|---|
#2: Chemical | ChemComp-K / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 52.51 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: sodium/potassium phosphate 2.4 M 20% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.458 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 12, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.458 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→48.02 Å / Num. obs: 31515 / % possible obs: 98 % / Redundancy: 4.56 % / CC1/2: 0.999 / Net I/σ(I): 13.47 |
Reflection shell | Resolution: 1.8→1.91 Å / Num. unique obs: 4570 / CC1/2: 0.691 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→28.28 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.955 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.11 / ESU R Free: 0.109 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: 102.91 Å2 / Biso mean: 32.528 Å2 / Biso min: 20.44 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.8→28.28 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.802→1.849 Å / Total num. of bins used: 20
|