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- PDB-7an1: A single sulfatase is required for metabolism of colonic mucin O-... -

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Basic information

Entry
Database: PDB / ID: 7an1
TitleA single sulfatase is required for metabolism of colonic mucin O-glycans and intestinal colonization by a symbiotic human gut bacterium (BT1636-S1_20)
ComponentsArylsulfatase
KeywordsHYDROLASE / Carbohydrate sulfatase / mucin / microbiome / bacteroides
Function / homology: / Sulfatases signature 1. / Sulfatase, conserved site / Sulfatase, N-terminal / Sulfatase / Alkaline-phosphatase-like, core domain superfamily / hydrolase activity / metal ion binding / Arylsulfatase
Function and homology information
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsSofia de Jesus Vaz Luis, A. / Basle, A. / Martens, E.C. / 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 10, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 27, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 3, 2021Group: Data collection / Category: pdbx_database_proc
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

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Assembly

Deposited unit
AAA: Arylsulfatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,4533
Polymers58,0291
Non-polymers4232
Water6,918384
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)74.280, 87.850, 103.310
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: 58029.316 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_1636 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8A789
#2: Polysaccharide beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 383.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a2112h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][b-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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 384 / 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: 2.9 Å3/Da / Density % sol: 57.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: BT1636 (20 mg/ml) with 20 mM LacNAc crystallised in 40 % MPD and 0.2 M sodium cacodylate pH 6.5.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jul 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.5→51.709 Å / Num. obs: 107725 / % possible obs: 99.1 % / Redundancy: 7 % / CC1/2: 0.997 / Net I/σ(I): 11.2
Reflection shellResolution: 1.5→1.53 Å / Mean I/σ(I) obs: 1.4 / Num. unique obs: 5296 / CC1/2: 0.656

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Processing

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

1fsu


Resolution: 1.5→51.708 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.973 / WRfactor Rfree: 0.172 / WRfactor Rwork: 0.143 / SU B: 3.819 / SU ML: 0.057 / Average fsc free: 0.9433 / Average fsc work: 0.957 / Cross valid method: FREE R-VALUE / ESU R: 0.057 / ESU R Free: 0.053
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1672 5546 5.152 %
Rwork0.1411 102096 -
all0.142 --
obs-107642 99.064 %
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: 24.081 Å2
Baniso -1Baniso -2Baniso -3
1-2.057 Å20 Å2-0 Å2
2---4.787 Å2-0 Å2
3---2.729 Å2
Refinement stepCycle: LAST / Resolution: 1.5→51.708 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3877 0 27 384 4288
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0134109
X-RAY DIFFRACTIONr_bond_other_d0.0020.0173706
X-RAY DIFFRACTIONr_angle_refined_deg1.5031.6545577
X-RAY DIFFRACTIONr_angle_other_deg1.41.5848596
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.345503
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.85623.288222
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.36915678
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.181517
X-RAY DIFFRACTIONr_chiral_restr0.0810.2509
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024746
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02964
X-RAY DIFFRACTIONr_nbd_refined0.210.2877
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1830.23611
X-RAY DIFFRACTIONr_nbtor_refined0.1730.21994
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.21755
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.2317
X-RAY DIFFRACTIONr_metal_ion_refined0.1190.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1850.26
X-RAY DIFFRACTIONr_nbd_other0.0950.214
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1870.214
X-RAY DIFFRACTIONr_mcbond_it2.6022.2411985
X-RAY DIFFRACTIONr_mcbond_other2.5972.2391984
X-RAY DIFFRACTIONr_mcangle_it3.3133.3732497
X-RAY DIFFRACTIONr_mcangle_other3.3153.3752498
X-RAY DIFFRACTIONr_scbond_it3.2252.5862124
X-RAY DIFFRACTIONr_scbond_other3.2262.5892125
X-RAY DIFFRACTIONr_scangle_it3.9173.7443080
X-RAY DIFFRACTIONr_scangle_other3.9173.7483081
X-RAY DIFFRACTIONr_lrange_it4.46927.7314811
X-RAY DIFFRACTIONr_lrange_other4.39227.444750
X-RAY DIFFRACTIONr_rigid_bond_restr4.05737815
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.5390.2994310.3227471X-RAY DIFFRACTION99.1468
1.539-1.5810.3154150.277339X-RAY DIFFRACTION99.9742
1.581-1.6270.2313400.2237186X-RAY DIFFRACTION99.9336
1.627-1.6770.233760.1876934X-RAY DIFFRACTION100
1.677-1.7320.2123580.1696745X-RAY DIFFRACTION100
1.732-1.7930.1923540.1456537X-RAY DIFFRACTION99.913
1.793-1.860.1793660.1366268X-RAY DIFFRACTION99.8495
1.86-1.9360.1733400.1316067X-RAY DIFFRACTION99.9064
1.936-2.0220.1692990.1345809X-RAY DIFFRACTION99.6086
2.022-2.1210.1792750.1385602X-RAY DIFFRACTION99.4248
2.121-2.2360.1572800.1215247X-RAY DIFFRACTION98.8907
2.236-2.3710.1552580.1144988X-RAY DIFFRACTION99.112
2.371-2.5350.1462690.1124682X-RAY DIFFRACTION98.7829
2.535-2.7380.1392470.1134327X-RAY DIFFRACTION97.7142
2.738-2.9990.182330.1263960X-RAY DIFFRACTION97.3758
2.999-3.3530.141960.1343607X-RAY DIFFRACTION96.867
3.353-3.8710.1321660.1273189X-RAY DIFFRACTION96.0492
3.871-4.7390.1351470.1152703X-RAY DIFFRACTION96.512
4.739-6.6950.1781260.1672171X-RAY DIFFRACTION97.7863
6.695-51.7080.176700.1871264X-RAY DIFFRACTION97.6574

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