- PDB-5wzr: Alpha-N-acetylgalactosaminidase NagBb from Bifidobacterium bifidu... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 5wzr
Title
Alpha-N-acetylgalactosaminidase NagBb from Bifidobacterium bifidum - Gal-NHAc-DNJ complex
Components
Alpha-N-acetylgalactosaminidase
Keywords
HYDROLASE / Glycoside Hydrolase
Function / homology
Protein of unknown function DUF5696 / Family of unknown function (DUF5696) / Endo-alpha-N-acetylgalactosaminidase / endo-alpha-N-acetylgalactosaminidase activity / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / metabolic process / metal ion binding / Chem-DJN / Alpha-N-acetylgalactosaminidase
Function and homology information
Biological species
Bifidobacterium bifidum (bacteria)
Method
X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.79 Å
Monochromator: Cryo-cooled channel-cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1.1 Å / Relative weight: 1
Reflection
Resolution: 2.79→103.95 Å / Num. obs: 37110 / % possible obs: 99.7 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 19.6
Reflection shell
Resolution: 2.79→2.85 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.518 / Mean I/σ(I) obs: 2.4 / CC1/2: 0.979 / % possible all: 100
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Processing
Software
Name
Version
Classification
REFMAC
5.8.0049
refinement
HKL-2000
datareduction
HKL-2000
datascaling
PHENIX
phasing
Refinement
Method to determine structure: SAD / Resolution: 2.79→103.95 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.864 / SU B: 24.947 / SU ML: 0.459 / Cross valid method: THROUGHOUT / ESU R Free: 0.476 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.31325
1852
5 %
RANDOM
Rwork
0.22899
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obs
0.23315
35202
98.66 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å