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Yorodumi- PDB-6kpm: Crystal Structure of endo-beta-N-acetylglucosaminidase from Cordy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6kpm | ||||||
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Title | Crystal Structure of endo-beta-N-acetylglucosaminidase from Cordyceps militaris in complex with L-fucose | ||||||
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: 1.8 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 | 6kpm.cif.gz | 75.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6kpm.ent.gz | 57.6 KB | Display | PDB format |
PDBx/mmJSON format | 6kpm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6kpm_validation.pdf.gz | 790.5 KB | Display | wwPDB validaton report |
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Full document | 6kpm_full_validation.pdf.gz | 791.1 KB | Display | |
Data in XML | 6kpm_validation.xml.gz | 15.6 KB | Display | |
Data in CIF | 6kpm_validation.cif.gz | 23.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kp/6kpm ftp://data.pdbj.org/pub/pdb/validation_reports/kp/6kpm | 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: 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 | ||||
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#2: Sugar | ChemComp-FUC / | ||||
#3: Chemical | ChemComp-PGE / | ||||
#4: Chemical | #5: 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: 3.04 Å3/Da / Density % sol: 59.6 % |
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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: BL-5A / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 24, 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: 1.8→50 Å / Num. obs: 37466 / % possible obs: 100 % / Redundancy: 6.7 % / CC1/2: 0.99 / Rmerge(I) obs: 0.101 / Net I/σ(I): 16.1 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.841 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 1851 / CC1/2: 0.816 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.8→45.86 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.958 / SU B: 2.567 / SU ML: 0.076 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.095 / ESU R Free: 0.098 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: 77.79 Å2 / Biso mean: 29.717 Å2 / Biso min: 19.16 Å2
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Refinement step | Cycle: final / Resolution: 1.8→45.86 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.844 Å / Rfactor Rfree error: 0
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