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- PDB-7lk7: Structure of the Exo-alpha-L-galactosidase BpGH29 from Bacteroide... -

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Basic information

Entry
Database: PDB / ID: 7lk7
TitleStructure of the Exo-alpha-L-galactosidase BpGH29 from Bacteroides plebeius in complex with L-galactose
ComponentsExo-alpha-L-galactosidase
KeywordsHYDROLASE / glycoside hydrolase / porphyran / carbohydrate
Function / homology
Function and homology information


alpha-L-fucosidase activity / fucose metabolic process / glycoside catabolic process / lysosome / metal ion binding
Similarity search - Function
Alpha-L-fucosidase, C-terminal / Alpha-L-fucosidase C-terminal domain / Alpha-L-fucosidase, metazoa-type / Alpha-L-fucosidase / Glycoside hydrolase, family 29 / Alpha-L-fucosidase / Glycosyl hydrolase, all-beta / Prokaryotic membrane lipoprotein lipid attachment site profile. / Glycoside hydrolase superfamily
Similarity search - Domain/homology
alpha-L-galactopyranose / Alpha-L-fucosidase
Similarity search - Component
Biological speciesBacteroides plebeius (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsBoraston, A.B. / Robb, C.S.
CitationJournal: Nat.Chem.Biol. / Year: 2022
Title: Metabolism of a hybrid algal galactan by members of the human gut microbiome.
Authors: Robb, C.S. / Hobbs, J.K. / Pluvinage, B. / Reintjes, G. / Klassen, L. / Monteith, S. / Giljan, G. / Amundsen, C. / Vickers, C. / Hettle, A.G. / Hills, R. / Xing, X. / Montina, T. / Zandberg, ...Authors: Robb, C.S. / Hobbs, J.K. / Pluvinage, B. / Reintjes, G. / Klassen, L. / Monteith, S. / Giljan, G. / Amundsen, C. / Vickers, C. / Hettle, A.G. / Hills, R. / Xing, X. / Montina, T. / Zandberg, W.F. / Abbott, D.W. / Boraston, A.B.
History
DepositionFeb 1, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 20, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 11, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Exo-alpha-L-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,6334
Polymers68,3501
Non-polymers2823
Water7,224401
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.156, 132.902, 54.486
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

#1: Protein Exo-alpha-L-galactosidase


Mass: 68350.328 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides plebeius (bacteria) / Strain: DSM 17135 / JCM 12973 / M2 / Gene: BACPLE_01702 / Production host: Escherichia coli (E. coli) / References: UniProt: B5CYA5
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Sugar ChemComp-GXL / alpha-L-galactopyranose / alpha-L-galactose / L-galactose / galactose


Type: L-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O6
IdentifierTypeProgram
LGalpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-L-galactopyranoseCOMMON NAMEGMML 1.0
a-L-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 401 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.58 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1 M BIS-TRIS (pH 5.5), 0.2 M (NH4)2SO4, 25% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 16, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.19→25 Å / Num. obs: 29901 / % possible obs: 99.9 % / Redundancy: 4.7 % / Biso Wilson estimate: 31.83 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 12.3
Reflection shellResolution: 2.19→2.27 Å / Rmerge(I) obs: 0.349 / Mean I/σ(I) obs: 3.6 / Num. unique obs: 2959

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
d*TREKdata scaling
d*TREKdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7LJJ

7ljj


Resolution: 2.19→19.95 Å / SU ML: 0.2744 / Cross valid method: FREE R-VALUE / σ(F): 0.27 / Phase error: 24.0292 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2301 1503 5.06 %
Rwork0.1814 28177 -
obs0.1838 29680 99.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.74 Å2
Refinement stepCycle: LAST / Resolution: 2.19→19.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4484 0 17 401 4902
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00254630
X-RAY DIFFRACTIONf_angle_d0.59046289
X-RAY DIFFRACTIONf_chiral_restr0.0446661
X-RAY DIFFRACTIONf_plane_restr0.0034806
X-RAY DIFFRACTIONf_dihedral_angle_d2.50623711
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.19-2.260.34681240.24522523X-RAY DIFFRACTION99.03
2.26-2.340.33561360.24022510X-RAY DIFFRACTION99.14
2.34-2.430.28621230.23982544X-RAY DIFFRACTION99.22
2.43-2.550.29481580.22672496X-RAY DIFFRACTION99.33
2.55-2.680.29781440.21982525X-RAY DIFFRACTION99.22
2.68-2.850.29211210.21832548X-RAY DIFFRACTION98.85
2.85-3.070.27591220.20712580X-RAY DIFFRACTION99.19
3.07-3.370.21350.1842552X-RAY DIFFRACTION99.15
3.37-3.860.19941410.15962589X-RAY DIFFRACTION99.53
3.86-4.850.18161550.13492583X-RAY DIFFRACTION99.27
4.85-19.950.18231440.15342727X-RAY DIFFRACTION98.73

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