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- PDB-7lj2: Structure of Exo-L-galactose-6-sulfatase BuS1_11 from Bacteroides... -

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Basic information

Entry
Database: PDB / ID: 7lj2
TitleStructure of Exo-L-galactose-6-sulfatase BuS1_11 from Bacteroides uniformis in complex with neoporphyrabiose
ComponentsExo-L-galactose-6-sulfatase
KeywordsHYDROLASE / sulfatase / porphyran / carbohydrate
Function / homology
Function and homology information


hydrolase activity / metal ion binding
Similarity search - Function
N-sulphoglucosamine sulphohydrolase, C-terminal / N-sulphoglucosamine sulphohydrolase, C-terminal / Sulfatases signature 2. / Sulfatases signature 1. / Sulfatase, conserved site / Sulfatase, N-terminal / Sulfatase / Alkaline-phosphatase-like, core domain superfamily
Similarity search - Domain/homology
Acetylglucosamine-6-sulfatase
Similarity search - Component
Biological speciesBacteroides uniformis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 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 28, 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

Downloads & links

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Assembly

Deposited unit
A: Exo-L-galactose-6-sulfatase
B: Exo-L-galactose-6-sulfatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,4808
Polymers124,5092
Non-polymers9716
Water9,602533
1
A: Exo-L-galactose-6-sulfatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,7404
Polymers62,2541
Non-polymers4853
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Exo-L-galactose-6-sulfatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,7404
Polymers62,2541
Non-polymers4853
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.670, 89.670, 267.060
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein Exo-L-galactose-6-sulfatase


Mass: 62254.398 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides uniformis (bacteria) / Gene: Bun01g_38470 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A4Y1VMZ7
#2: Polysaccharide 6-O-sulfo-alpha-L-galactopyranose-(1-3)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 422.360 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LGalp[6S]a1-3DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2112h-1b_1-5][a1221h-1a_1-5_6*OSO/3=O/3=O]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[][b-D-Galp]{[(3+1)][a-L-Galp6SO3]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Ca
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 533 / 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: 2.16 Å3/Da / Density % sol: 42.95 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1 M HEPES (pH 7.5), 0.2 M MgCl2, 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: Jul 16, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 42974 / % possible obs: 98.6 % / Redundancy: 3.3 % / Biso Wilson estimate: 39.08 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.063 / Net I/σ(I): 7.7
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 0.492 / Num. unique obs: 4494 / CC1/2: 0.729 / Rpim(I) all: 0.313

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7LHA

7lha


Resolution: 2.4→29.79 Å / SU ML: 0.341 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.1967 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2305 2129 4.96 %
Rwork0.1824 40752 -
obs0.1848 42881 98.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.12 Å2
Refinement stepCycle: LAST / Resolution: 2.4→29.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8241 0 58 533 8832
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0028586
X-RAY DIFFRACTIONf_angle_d0.553311647
X-RAY DIFFRACTIONf_chiral_restr0.04241211
X-RAY DIFFRACTIONf_plane_restr0.00341507
X-RAY DIFFRACTIONf_dihedral_angle_d4.77757109
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.460.37141510.26522674X-RAY DIFFRACTION99.33
2.46-2.520.28281360.24582701X-RAY DIFFRACTION99.47
2.52-2.590.30591530.23532678X-RAY DIFFRACTION99.3
2.59-2.660.29351190.22422711X-RAY DIFFRACTION99.33
2.66-2.750.281190.21682738X-RAY DIFFRACTION99.24
2.75-2.850.24421560.21172681X-RAY DIFFRACTION99.27
2.85-2.960.25351490.20092701X-RAY DIFFRACTION99.16
2.96-3.090.28411590.212714X-RAY DIFFRACTION98.93
3.09-3.260.27721450.19792685X-RAY DIFFRACTION98.92
3.26-3.460.25011560.19222713X-RAY DIFFRACTION98.76
3.46-3.730.22421380.18552730X-RAY DIFFRACTION98.35
3.73-4.10.21031220.15852746X-RAY DIFFRACTION97.75
4.1-4.690.1721490.14622721X-RAY DIFFRACTION97.19
4.69-5.90.19981430.14912721X-RAY DIFFRACTION95.95
5.9-29.790.17411340.16162838X-RAY DIFFRACTION93.25

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