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Yorodumi- PDB-6kpn: Crystal Structure of endo-beta-N-acetylglucosaminidase from Cordy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6kpn | |||||||||
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Title | Crystal Structure of endo-beta-N-acetylglucosaminidase from Cordyceps militaris D154N/E156Q mutant in complex with fucosyl-N-acetylglucosamine | |||||||||
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: 2.1 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6kpn.cif.gz | 71.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6kpn.ent.gz | 54.3 KB | Display | PDB format |
PDBx/mmJSON format | 6kpn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6kpn_validation.pdf.gz | 741.7 KB | Display | wwPDB validaton report |
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Full document | 6kpn_full_validation.pdf.gz | 743.3 KB | Display | |
Data in XML | 6kpn_validation.xml.gz | 14.1 KB | Display | |
Data in CIF | 6kpn_validation.cif.gz | 19.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kp/6kpn ftp://data.pdbj.org/pub/pdb/validation_reports/kp/6kpn | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 33402.316 Da / Num. of mol.: 1 / Mutation: D154N, E156Q 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 |
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#2: Polysaccharide | alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.05 Å3/Da / Density % sol: 59.72 % |
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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 |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Dec 2, 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 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→45.78 Å / Num. obs: 23548 / % possible obs: 99.9 % / Redundancy: 5.1 % / CC1/2: 0.996 / Rmerge(I) obs: 0.141 / Net I/σ(I): 8 |
Reflection shell | Resolution: 2.1→2.16 Å / Redundancy: 5.2 % / Rmerge(I) obs: 1.241 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 1915 / CC1/2: 0.484 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.1→19.98 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.94 / SU B: 7.991 / SU ML: 0.185 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.185 / ESU R Free: 0.172 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 102.44 Å2 / Biso mean: 40.472 Å2 / Biso min: 24.48 Å2
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Refinement step | Cycle: final / Resolution: 2.1→19.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.103→2.157 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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