- PDB-5wzp: 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: 5wzp
Title
Alpha-N-acetylgalactosaminidase NagBb from Bifidobacterium bifidum - ligand free
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 / Alpha-N-acetylgalactosaminidase
Function and homology information
Biological species
Bifidobacterium bifidum (bacteria)
Method
X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.64 Å
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: 2.64→103.55 Å / Num. obs: 42830 / % possible obs: 99.6 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 18.3
Reflection shell
Resolution: 2.65→2.7 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.627 / Mean I/σ(I) obs: 1.9 / CC1/2: 0.849 / % possible all: 99.2
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Processing
Software
Name
Version
Classification
REFMAC
5.8.0158
refinement
HKL-2000
datareduction
HKL-2000
datascaling
PHENIX
phasing
Refinement
Method to determine structure: SAD / Resolution: 2.64→103.55 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.869 / Cross valid method: THROUGHOUT / ESU R: 1.37 / ESU R Free: 0.409 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.31098
2114
4.9 %
RANDOM
Rwork
0.23053
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obs
0.23453
40656
99.07 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK