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

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Basic information

Entry
Database: PDB / ID: 7ljj
TitleStructure of the Exo-alpha-L-galactosidase BpGH29 from Bacteroides plebeius
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
Biological speciesBacteroides plebeius (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsRobb, C.S. / Boraston, A.B.
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
DepositionJan 29, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 30, 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)68,5775
Polymers68,3501
Non-polymers2264
Water12,142674
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.010, 76.430, 132.380
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-1370-

HOH

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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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 674 / 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: 40.66 %
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: Jun 19, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→26 Å / Num. obs: 45650 / % possible obs: 100 % / Redundancy: 4.7 % / Biso Wilson estimate: 19.15 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.042 / Net I/σ(I): 15.4
Reflection shellResolution: 1.9→1.94 Å / Rmerge(I) obs: 0.516 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 3045 / CC1/2: 0.835 / Rpim(I) all: 0.271

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2wvu

2wvu


Resolution: 1.9→25.79 Å / SU ML: 0.1876 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 18.7402 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2082 2301 5.05 %
Rwork0.1597 43294 -
obs0.1621 45595 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.99 Å2
Refinement stepCycle: LAST / Resolution: 1.9→25.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4498 0 13 674 5185
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00644630
X-RAY DIFFRACTIONf_angle_d0.79646269
X-RAY DIFFRACTIONf_chiral_restr0.0546649
X-RAY DIFFRACTIONf_plane_restr0.0049803
X-RAY DIFFRACTIONf_dihedral_angle_d3.05582703
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.940.25671610.21452670X-RAY DIFFRACTION100
1.94-1.990.27251570.1892626X-RAY DIFFRACTION100
1.99-2.040.22571110.18262708X-RAY DIFFRACTION100
2.04-2.090.25421430.18472647X-RAY DIFFRACTION100
2.09-2.150.2411400.17552710X-RAY DIFFRACTION100
2.15-2.220.23591360.16742660X-RAY DIFFRACTION99.96
2.22-2.30.21351570.16182650X-RAY DIFFRACTION100
2.3-2.390.22851640.15912665X-RAY DIFFRACTION99.93
2.39-2.50.20571440.15962694X-RAY DIFFRACTION99.86
2.5-2.630.22981330.16172709X-RAY DIFFRACTION100
2.63-2.80.22431340.16392705X-RAY DIFFRACTION100
2.8-3.010.20221230.16682720X-RAY DIFFRACTION100
3.01-3.320.22611470.16212733X-RAY DIFFRACTION100
3.32-3.80.19251740.1432702X-RAY DIFFRACTION100
3.8-4.780.15811420.13042780X-RAY DIFFRACTION100
4.78-250.17111350.15862915X-RAY DIFFRACTION99.93

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