- PDB-5jox: Bacteroides ovatus Xyloglucan PUL GH43A in complex with AraDNJ -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 5jox
Title
Bacteroides ovatus Xyloglucan PUL GH43A in complex with AraDNJ
Components
Non-reducing end alpha-L-arabinofuranosidase BoGH43A
Keywords
HYDROLASE / Glycoside hydrolase / GH43
Function / homology
Function and homology information
symbiotic process benefiting host / xyloglucan catabolic process / non-reducing end alpha-L-arabinofuranosidase / alpha-L-arabinofuranosidase activity / periplasmic space Similarity search - Function
Mass: 18.015 Da / Num. of mol.: 1005 / Source method: isolated from a natural source / Formula: H2O
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 2.31 Å3/Da / Density % sol: 46.74 %
Crystal grow
Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: 0.1 M Tris pH 7.2 - 7.8, 0.18 M magnesium chloride and 12% (w/v) PEG-6000
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.9795 Å / Relative weight: 1
Reflection
Resolution: 1.8→46.58 Å / Num. obs: 100168 / % possible obs: 99.9 % / Redundancy: 7.5 % / CC1/2: 0.994 / Rmerge(I) obs: 0.128 / Net I/σ(I): 8.5
Reflection shell
Resolution: 1.8→1.83 Å / Redundancy: 7.2 % / Rmerge(I) obs: 1.14 / Mean I/σ(I) obs: 1.2 / % possible all: 100
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Processing
Software
Name
Version
Classification
REFMAC
5.8.0124
refinement
XDS
datareduction
Aimless
datascaling
PHASER
phasing
Refinement
Method to determine structure: MOLECULAR REPLACEMENT Starting model: GH43B to be deposited Resolution: 1.8→46.58 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.944 / SU B: 3.489 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.129 / ESU R Free: 0.122 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.21618
5020
5 %
RANDOM
Rwork
0.17982
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obs
0.18164
95085
99.85 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å