+Open data
-Basic information
Entry | Database: PDB / ID: 3wdv | |||||||||
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Title | The complex structure of PtLic16A with cellotetraose | |||||||||
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: 1.936 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3wdv.cif.gz | 266.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3wdv.ent.gz | 212.7 KB | Display | PDB format |
PDBx/mmJSON format | 3wdv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wd/3wdv ftp://data.pdbj.org/pub/pdb/validation_reports/wd/3wdv | HTTPS FTP |
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-Related structure data
Related structure data | 3wdtSC 3wduC 3wdwC 3wdxC 3wdyC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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Unit cell |
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-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: Polysaccharide | beta-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-cellobiose #3: Sugar | #4: Chemical | ChemComp-SO4 / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.36 % |
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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 |
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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: 1.92→25 Å / Num. obs: 94075 / % possible obs: 100 % / Redundancy: 6 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 15.8 |
Reflection shell | Resolution: 1.92→1.99 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.488 / Mean I/σ(I) obs: 2.6 / Num. unique all: 9289 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3WDT Resolution: 1.936→25 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 35.3406 Å2 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.2452 Å2
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Refinement step | Cycle: LAST / Resolution: 1.936→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.936→1.99 Å /
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