[English] 日本語
Yorodumi- PDB-7ncx: Crystal structure of GH30 (double mutant EE) from Thermothelomyce... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ncx | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of GH30 (double mutant EE) from Thermothelomyces thermophila. | ||||||
Components | GH30 family xylanase | ||||||
Keywords | HYDROLASE / xylanase / GH30 / subfamily 7 | ||||||
Function / homology | Function and homology information glucosylceramidase activity / sphingolipid metabolic process / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / extracellular region Similarity search - Function | ||||||
Biological species | Myceliophthora thermophila (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.36 Å | ||||||
Authors | Dimarogona, M. / Nikolaivits, E. / Topakas, E. / Weiss, M. / Feiler, C.G. | ||||||
Citation | Journal: Carbohydrate Polymers / Year: 2021 Title: Unique features of the bifunctional GH30 from Thermothelomyces thermophila revealed by structural and mutational studies Authors: Nikolaivits, E. / Pentari, C. / Kosinas, C. / Feiler, C.G. / Spiliopoulou, M. / Weiss, M.S. / Dimarogona, M. / Topakas, E. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7ncx.cif.gz | 341 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7ncx.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7ncx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nc/7ncx ftp://data.pdbj.org/pub/pdb/validation_reports/nc/7ncx | HTTPS FTP |
---|
-Related structure data
Related structure data | 7o0eC 6krlS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 1 molecules AAA
#1: Protein | Mass: 51728.941 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Myceliophthora thermophila (strain ATCC 42464 / BCRC 31852 / DSM 1799) (fungus) Strain: ATCC 42464 / BCRC 31852 / DSM 1799 / Gene: Xyn30A, MYCTH_38558 / Production host: Komagataella pastoris (fungus) References: UniProt: G2Q1N4, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds |
---|
-Sugars , 2 types, 2 molecules
#2: Polysaccharide | alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D- ...alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
---|---|
#6: Sugar | ChemComp-NAG / |
-Non-polymers , 4 types, 519 molecules
#3: Chemical | ChemComp-GOL / | ||
---|---|---|---|
#4: Chemical | ChemComp-PEG / | ||
#5: Chemical | #7: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | N |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.94 Å3/Da / Density % sol: 30.54 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG1500, TBG buffer |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 7, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.36→45.9 Å / Num. obs: 79578 / % possible obs: 99.7 % / Redundancy: 12.1 % / CC1/2: 1 / Net I/σ(I): 19.8 |
Reflection shell | Resolution: 1.36→1.38 Å / Num. unique obs: 3715 / CC1/2: 0.539 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6KRL Resolution: 1.36→43.696 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.973 / SU B: 2.093 / SU ML: 0.036 / Cross valid method: FREE R-VALUE / ESU R: 0.055 / ESU R Free: 0.051 Details: Hydrogens have been added in their riding positions
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.592 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.36→43.696 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|