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- PDB-5by3: A novel family GH115 4-O-Methyl-alpha-glucuronidase, BtGH115A, wi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5by3 | ||||||
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Title | A novel family GH115 4-O-Methyl-alpha-glucuronidase, BtGH115A, with specificity for decorated arabinogalactans | ||||||
![]() | BtGH115A | ||||||
![]() | SUGAR BINDING PROTEIN / Glycoside / hydrolase / arabinogalactans alpha-glucuronidase | ||||||
Function / homology | Glycosyl hydrolase family 115 / Gylcosyl hydrolase 115 C-terminal domain / Glycosyl hydrolase 115 superfamily / Glycosyl hydrolase family 115 / Gylcosyl hydrolase family 115 C-terminal domain / Beta-hexosaminidase-like, domain 2 / hydrolase activity / NICKEL (II) ION / GH115_C domain-containing protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Lammerts van Bueren, A. / Davies, G.J. / Turkenburg, J.P. | ||||||
![]() | ![]() Title: Structural and Functional Characterization of a Novel Family GH115 4-O-Methyl-alpha-Glucuronidase with Specificity for Decorated Arabinogalactans. Authors: Aalbers, F. / Turkenburg, J.P. / Davies, G.J. / Dijkhuizen, L. / Lammerts van Bueren, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 164.3 KB | Display | ![]() |
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PDB format | ![]() | 134.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 447 KB | Display | ![]() |
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Full document | ![]() | 458.4 KB | Display | |
Data in XML | ![]() | 28.7 KB | Display | |
Data in CIF | ![]() | 39.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 89923.984 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: BT_2958 / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-SO4 / |
#3: Chemical | ChemComp-NI / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 53.6 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 3.5 / Details: 20% PEG 3350 0.2M sodium sulfate 0.01M glycine |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 4, 2011 | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.44→40 Å / Num. obs: 32214 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 4.6 % / Net I/σ(I): 17.6 | ||||||||||||
Reflection shell | Resolution: 2.44→2.51 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.614 / Mean I/σ(I) obs: 2.8 / % possible all: 99.9 |
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Processing
Software | Name: REFMAC / Version: 5.8.0103 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 2.44→40 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.91 / SU B: 10.658 / SU ML: 0.239 / Cross valid method: THROUGHOUT / ESU R: 0.487 / ESU R Free: 0.298 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 53.628 Å2
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Refinement step | Cycle: LAST / Resolution: 2.44→40 Å
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Refine LS restraints |
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