- PDB-6kpl: Crystal Structure of endo-beta-N-acetylglucosaminidase from Cordy... -
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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
Glycosyl hydrolases family 18 (GH18) active site / Glycosyl hydrolases family 18 (GH18) active site signature. / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycoside hydrolase family 18, catalytic domain / Glycosyl hydrolases family 18 / Glycoside hydrolase superfamily Similarity search - Domain/homology
#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.
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
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Processing
Software
Name
Version
Classification
REFMAC
5.8.0238
refinement
PDB_EXTRACT
3.25
dataextraction
HKL-2000
datareduction
HKL-2000
datascaling
PHENIX
phasing
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
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.1843
2131
5.2 %
RANDOM
Rwork
0.1552
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obs
0.1567
38543
99.79 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
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