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- PDB-7all: A single sulfatase is required for metabolism of colonic mucin O-... -

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Basic information

Entry
Database: PDB / ID: 7all
TitleA single sulfatase is required for metabolism of colonic mucin O-glycans and intestinal colonization by a symbiotic human gut bacterium (BT4683-S1_4)
ComponentsArylsulfatase
KeywordsHYDROLASE / Carbohydrate sulfatase / Mucin / Microbiome / Bacteroides
Function / homology
Function and homology information


arylsulfatase activity / metal ion binding
Similarity search - Function
: / Sulfatases signature 2. / Sulfatase, conserved site / Sulfatase, N-terminal / Sulfatase / Alkaline-phosphatase-like, core domain superfamily
Similarity search - Domain/homology
N-acetyl-alpha-lactosamine / IODIDE ION / Arylsulfatase
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å
AuthorsSofia de Jesus Vaz Luis, A. / Martens, E.C. / Basle, A. / Cartmell, A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome TrustSBF0051065163470 United Kingdom
CitationJournal: Nature / Year: 2021
Title: A single sulfatase is required to access colonic mucin by a gut bacterium.
Authors: Luis, A.S. / Jin, C. / Pereira, G.V. / Glowacki, R.W.P. / Gugel, S.R. / Singh, S. / Byrne, D.P. / Pudlo, N.A. / London, J.A. / Basle, A. / Reihill, M. / Oscarson, S. / Eyers, P.A. / Czjzek, ...Authors: Luis, A.S. / Jin, C. / Pereira, G.V. / Glowacki, R.W.P. / Gugel, S.R. / Singh, S. / Byrne, D.P. / Pudlo, N.A. / London, J.A. / Basle, A. / Reihill, M. / Oscarson, S. / Eyers, P.A. / Czjzek, M. / Michel, G. / Barbeyron, T. / Yates, E.A. / Hansson, G.C. / Karlsson, N.G. / Cartmell, A. / Martens, E.C.
History
DepositionOct 6, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 13, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 3, 2021Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Arylsulfatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,3997
Polymers59,4681
Non-polymers9316
Water5,567309
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.136, 87.799, 101.833
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Arylsulfatase


Mass: 59468.293 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482) (bacteria)
Strain: ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482 / Gene: BT_4683 / Production host: Escherichia coli (E. coli) / References: UniProt: Q89YP8
#2: Polysaccharide beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Glycan component / Mass: 383.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: N-acetyl-alpha-lactosamine
DescriptorTypeProgram
DGalpb1-4DGlcpNAca1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1a_1-5_2*NCC/3=O][a2112h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: I
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 309 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 40.65 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 20 % PEG 3350, 0.2 M sodium iodide and BTP pH 8.5 25mg/ml

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Feb 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.63→66.585 Å / Num. obs: 62376 / % possible obs: 99.9 % / Redundancy: 1.9 % / CC1/2: 0.999 / Net I/σ(I): 7.8
Reflection shellResolution: 1.63→1.66 Å / Mean I/σ(I) obs: 1.4 / Num. unique obs: 3024 / CC1/2: 0.795

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
xia2data reduction
xia2data scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HDH

1hdh


Resolution: 1.63→66.585 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.954 / WRfactor Rfree: 0.196 / WRfactor Rwork: 0.17 / SU B: 2.437 / SU ML: 0.078 / Average fsc free: 0.8918 / Average fsc work: 0.8974 / Cross valid method: FREE R-VALUE / ESU R: 0.094 / ESU R Free: 0.09
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2003 3095 4.962 %
Rwork0.174 59281 -
all0.175 --
obs-62376 99.896 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 22.124 Å2
Baniso -1Baniso -2Baniso -3
1--1.456 Å20 Å20 Å2
2---1.189 Å2-0 Å2
3---2.645 Å2
Refinement stepCycle: LAST / Resolution: 1.63→66.585 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3991 0 31 309 4331
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0134198
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173859
X-RAY DIFFRACTIONr_angle_refined_deg1.531.6585703
X-RAY DIFFRACTIONr_angle_other_deg1.3891.5828959
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9775513
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.322.605215
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.33915714
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5071522
X-RAY DIFFRACTIONr_chiral_restr0.0770.2543
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024759
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02965
X-RAY DIFFRACTIONr_nbd_refined0.2030.2889
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1780.23652
X-RAY DIFFRACTIONr_nbtor_refined0.1720.22032
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0750.21883
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.2248
X-RAY DIFFRACTIONr_metal_ion_refined0.2510.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1630.211
X-RAY DIFFRACTIONr_nbd_other0.2020.247
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1580.215
X-RAY DIFFRACTIONr_mcbond_it1.5182.1332031
X-RAY DIFFRACTIONr_mcbond_other1.5042.1322030
X-RAY DIFFRACTIONr_mcangle_it2.1423.1962551
X-RAY DIFFRACTIONr_mcangle_other2.1463.1962552
X-RAY DIFFRACTIONr_scbond_it2.5552.4242167
X-RAY DIFFRACTIONr_scbond_other2.5542.4262168
X-RAY DIFFRACTIONr_scangle_it3.9213.5253152
X-RAY DIFFRACTIONr_scangle_other3.923.5273153
X-RAY DIFFRACTIONr_lrange_it4.73325.5074864
X-RAY DIFFRACTIONr_lrange_other4.66525.334819
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.63-1.6720.2912270.2844331X-RAY DIFFRACTION99.8467
1.672-1.7180.2832070.2584210X-RAY DIFFRACTION100
1.718-1.7680.252170.2454097X-RAY DIFFRACTION100
1.768-1.8220.2292050.2223989X-RAY DIFFRACTION100
1.822-1.8820.2442100.2023877X-RAY DIFFRACTION100
1.882-1.9480.2231980.1763748X-RAY DIFFRACTION100
1.948-2.0220.2041760.1613631X-RAY DIFFRACTION100
2.022-2.1040.2241960.1713481X-RAY DIFFRACTION100
2.104-2.1980.2071760.1563385X-RAY DIFFRACTION100
2.198-2.3050.1811700.1573206X-RAY DIFFRACTION100
2.305-2.4290.1781610.1523053X-RAY DIFFRACTION100
2.429-2.5770.2061540.1612886X-RAY DIFFRACTION100
2.577-2.7540.1821350.152765X-RAY DIFFRACTION100
2.754-2.9750.1841310.1622548X-RAY DIFFRACTION100
2.975-3.2590.1871240.1762361X-RAY DIFFRACTION100
3.259-3.6430.2061050.1742160X-RAY DIFFRACTION100
3.643-4.2050.1711010.1511904X-RAY DIFFRACTION100
4.205-5.1480.15970.1441622X-RAY DIFFRACTION100
5.148-7.2720.209620.1961304X-RAY DIFFRACTION100
7.272-66.5850.258430.204723X-RAY DIFFRACTION95.5112

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