[English] 日本語
Yorodumi- PDB-6kpl: Crystal Structure of endo-beta-N-acetylglucosaminidase from Cordy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6kpl | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of endo-beta-N-acetylglucosaminidase from Cordyceps militaris in apo form | ||||||
Components | Chitinase | ||||||
Keywords | HYDROLASE / TIM barrel | ||||||
Function / homology | Function and homology information chitinase activity / chitin catabolic process / polysaccharide catabolic process / extracellular region Similarity search - Function | ||||||
Biological species | Cordyceps militaris CM01 (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.75 Å | ||||||
Authors | Seki, H. / Arakawa, T. / Yamada, C. / Takegawa, K. / Fushinobu, S. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2019 Title: Structural basis for the specific cleavage of core-fucosylatedN-glycans by endo-beta-N-acetylglucosaminidase from the fungusCordyceps militaris. Authors: Seki, H. / Huang, Y. / Arakawa, T. / Yamada, C. / Kinoshita, T. / Iwamoto, S. / Higuchi, Y. / Takegawa, K. / Fushinobu, S. #1: Journal: Sci Rep / Year: 2018 Title: Characterization of novel endo-beta-N-acetylglucosaminidases from Sphingobacterium species, Beauveria bassiana and Cordyceps militaris that specifically hydrolyze fucose-containing oligosaccharides and human IgG. Authors: Huang, Y. / Higuchi, Y. / Kinoshita, T. / Mitani, A. / Eshima, Y. / Takegawa, K. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6kpl.cif.gz | 74.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6kpl.ent.gz | 57.9 KB | Display | PDB format |
PDBx/mmJSON format | 6kpl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6kpl_validation.pdf.gz | 430 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6kpl_full_validation.pdf.gz | 430.5 KB | Display | |
Data in XML | 6kpl_validation.xml.gz | 15.6 KB | Display | |
Data in CIF | 6kpl_validation.cif.gz | 23.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kp/6kpl ftp://data.pdbj.org/pub/pdb/validation_reports/kp/6kpl | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 33404.289 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cordyceps militaris CM01 (fungus) / Strain: CM01 / Gene: CCM_08020 / Plasmid: pET-32b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): CodonPlus (DE3)-RIL / References: UniProt: G3JPF7 | ||||
---|---|---|---|---|---|
#2: Chemical | ChemComp-PGE / | ||||
#3: Chemical | #4: 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: 3.05 Å3/Da / Density % sol: 59.69 % |
---|---|
Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 8.6 / Details: 0.1 M CHES-NaOH (pH 8.6) and 20 % PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Feb 4, 2018 |
Radiation | Monochromator: Numerical link type Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→50 Å / Num. obs: 40703 / % possible obs: 100 % / Redundancy: 10.3 % / CC1/2: 0.991 / Rmerge(I) obs: 0.12 / Net I/σ(I): 23.9 |
Reflection shell | Resolution: 1.75→1.78 Å / Redundancy: 10.4 % / Rmerge(I) obs: 0.801 / Mean I/σ(I) obs: 3 / Num. unique obs: 2026 / CC1/2: 0.863 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 1.75→40.59 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.803 / SU ML: 0.057 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.084 / ESU R Free: 0.085 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: 72.11 Å2 / Biso mean: 22.863 Å2 / Biso min: 13.47 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.75→40.59 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.75→1.794 Å / Rfactor Rfree error: 0
|