[English] 日本語
Yorodumi- PDB-6uqj: Crystal structure of the GH39 enzyme from Xanthomonas axonopodis ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6uqj | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the GH39 enzyme from Xanthomonas axonopodis pv. citri | ||||||
Components | Beta-xylosidaseXylan 1,4-b-xylosidase | ||||||
Keywords | HYDROLASE / glycoside hydrolase family 39 | ||||||
Function / homology | Glycosyl hydrolases family 39 active site. / Glycoside hydrolase, family 39 / Glycosyl hydrolases family 39 / hydrolase activity, hydrolyzing O-glycosyl compounds / Glycoside hydrolase superfamily / carbohydrate metabolic process / Beta-xylosidase Function and homology information | ||||||
Biological species | Xanthomonas axonopodis pv. citri (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.707 Å | ||||||
Authors | Morais, M.A.B. / Polo, C.C. / Santos, C.R. / Murakami, M.T. | ||||||
Funding support | Brazil, 1items
| ||||||
Citation | Journal: Front Bioeng Biotechnol / Year: 2020 Title: Exploring the Molecular Basis for Substrate Affinity and Structural Stability in Bacterial GH39 beta-Xylosidases. Authors: de Morais, M.A.B. / Polo, C.C. / Domingues, M.N. / Persinoti, G.F. / Pirolla, R.A.S. / de Souza, F.H.M. / Correa, J.B.L. / Dos Santos, C.R. / Murakami, M.T. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6uqj.cif.gz | 127.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6uqj.ent.gz | 94.5 KB | Display | PDB format |
PDBx/mmJSON format | 6uqj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uq/6uqj ftp://data.pdbj.org/pub/pdb/validation_reports/uq/6uqj | HTTPS FTP |
---|
-Related structure data
Related structure data | 4ekjS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 57439.848 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xanthomonas axonopodis pv. citri (strain 306) (bacteria) Strain: 306 / Gene: xynB, XAC4058 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8PFC5 |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.38 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1 M MIB Buffer pH 5.0 and 25% (w/v) PEG 1500 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.459 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 21, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.459 Å / Relative weight: 1 |
Reflection | Resolution: 1.707→38.67 Å / Num. obs: 54724 / % possible obs: 98.21 % / Redundancy: 6 % / CC1/2: 0.999 / Net I/σ(I): 20.09 |
Reflection shell | Resolution: 1.707→1.768 Å / Num. unique obs: 5211 / CC1/2: 0.848 |
-Phasing
Phasing | Method: molecular replacement |
---|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4EKJ Resolution: 1.707→28.93 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.82
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 73.59 Å2 / Biso mean: 23.81 Å2 / Biso min: 12.56 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.707→28.93 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
|