+Open data
-Basic information
Entry | Database: PDB / ID: 3wdt | ||||||
---|---|---|---|---|---|---|---|
Title | The apo-form structure of PtLic16A from Paecilomyces thermophila | ||||||
Components | Beta-1,3-1,4-glucanaseEndo-1,3(4)-b-glucanase | ||||||
Keywords | HYDROLASE / 1 / 3-1 / 4-beta-glucanase / 3(4)-beta-glucanase / PtLic16A / beta-jellyroll fold | ||||||
Function / homology | Function and homology information licheninase activity / licheninase / side of membrane / carbohydrate metabolic process / plasma membrane Similarity search - Function | ||||||
Biological species | Paecilomyces (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å | ||||||
Authors | Cheng, Y.S. / Huang, C.H. / Chen, C.C. / Huang, T.Y. / Ko, T.P. / Huang, J.W. / Wu, T.H. / Liu, J.R. / Guo, R.T. | ||||||
Citation | Journal: Biochim.Biophys.Acta / Year: 2014 Title: Structural and mutagenetic analyses of a 1,3-1,4-beta-glucanase from Paecilomyces thermophila Authors: Cheng, Y.S. / Huang, C.H. / Chen, C.C. / Huang, T.Y. / Ko, T.P. / Huang, J.W. / Wu, T.H. / Liu, J.R. / Guo, R.T. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3wdt.cif.gz | 244.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3wdt.ent.gz | 196.6 KB | Display | PDB format |
PDBx/mmJSON format | 3wdt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wd/3wdt ftp://data.pdbj.org/pub/pdb/validation_reports/wd/3wdt | HTTPS FTP |
---|
-Related structure data
Related structure data | 3wduC 3wdvC 3wdwC 3wdxC 3wdyC 2w39S C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
4 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 32224.182 Da / Num. of mol.: 4 / Fragment: UNP residues 19-314 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Paecilomyces (fungus) / Strain: J18 / Plasmid: pPICZalphaA / Production host: Komagataella pastoris (fungus) / Strain (production host): X33 / References: UniProt: E0XN39, licheninase #2: Chemical | ChemComp-SO4 / | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.31 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2M ammonium sulfate, 0.1M sodium cacodylate, 30%(w/v) PEG8000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 13, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.98→25 Å / Num. obs: 89077 / % possible obs: 100 % / Redundancy: 12.3 % / Rmerge(I) obs: 0.114 |
Reflection shell | Resolution: 1.98→2.05 Å / Redundancy: 12.4 % / Rmerge(I) obs: 0.494 / Mean I/σ(I) obs: 4.3 / Num. unique all: 8786 / % possible all: 100 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2W39 Resolution: 1.98→25 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||
Solvent computation | Bsol: 35.7697 Å2 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.9601 Å2
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.98→25 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
LS refinement shell | Resolution: 1.98→2.05 Å /
|