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- PDB-7oza: Sulfated host glycan recognition by carbohydrate sulfatases of th... -

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Basic information

Entry
Database: PDB / ID: 7oza
TitleSulfated host glycan recognition by carbohydrate sulfatases of the human gut microbiota (BT3796_S1_16)
ComponentsPutative secreted sulfatase ydeN
KeywordsHYDROLASE / Host glycans / sulfation / carbohydrate sulfatases / microbiota
Function / homologyarylsulfatase activity / Sulfatases signature 1. / Sulfatase, conserved site / Sulfatase, N-terminal / Sulfatase / Alkaline-phosphatase-like, core domain superfamily / 4-O-sulfo-beta-D-galactopyranose / Putative secreted sulfatase ydeN
Function and homology information
Biological speciesBacteroides thetaiotaomicron VPI-5482 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsCartmell, A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
CitationJournal: Nat.Chem.Biol. / Year: 2022
Title: Sulfated glycan recognition by carbohydrate sulfatases of the human gut microbiota.
Authors: Luis, A.S. / Basle, A. / Byrne, D.P. / Wright, G.S.A. / London, J.A. / Jin, C. / Karlsson, N.G. / Hansson, G.C. / Eyers, P.A. / Czjzek, M. / Barbeyron, T. / Yates, E.A. / Martens, E.C. / Cartmell, A.
History
DepositionJun 27, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 29, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 10, 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 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Putative secreted sulfatase ydeN
CCC: Putative secreted sulfatase ydeN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,28311
Polymers117,4442
Non-polymers2,8399
Water13,601755
1
AAA: Putative secreted sulfatase ydeN
hetero molecules


  • defined by author
  • Evidence: light scattering
  • 59.3 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)59,3054
Polymers58,7221
Non-polymers5833
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
CCC: Putative secreted sulfatase ydeN
hetero molecules


  • defined by author
  • 61 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)60,9787
Polymers58,7221
Non-polymers2,2566
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.180, 88.950, 87.910
Angle α, β, γ (deg.)90.000, 112.050, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11AAA
21CCC

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: GLU / End label comp-ID: GLU / Auth seq-ID: 31 - 516 / Label seq-ID: 35 - 520

Dom-IDComponent-IDAuth asym-IDLabel asym-ID
11AAAA
22CCCB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

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Protein / Sugars , 2 types, 4 molecules AAACCC

#1: Protein Putative secreted sulfatase ydeN


Mass: 58722.207 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron VPI-5482 (bacteria)
Gene: BT_3796 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold / References: UniProt: Q8A171
#3: Sugar ChemComp-G4S / 4-O-sulfo-beta-D-galactopyranose / 4-O-sulfo-beta-D-galactose / 4-O-sulfo-D-galactose / 4-O-sulfo-galactose


Type: D-saccharide, beta linking / Mass: 260.219 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O9S / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGalp[4S]bCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
4-sulfo-b-D-galactopyranoseCOMMON NAMEGMML 1.0
b-D-Galp4SO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 6 types, 762 molecules

#2: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#6: Chemical ChemComp-15P / POLYETHYLENE GLYCOL (N=34) / PEG 1500 / Polyethylene glycol


Mass: 1529.829 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C69H140O35 / Comment: precipitant*YM
#7: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 755 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.26 Å3/Da / Density % sol: 45.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20 mg/ml BT3796S1_16 with 10mM 4S-GalNAc was crystallised in 20 % PEG 6000, 0.2 M magnesium chloride and 0.1 MES pH 6.0.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9159 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9159 Å / Relative weight: 1
ReflectionResolution: 1.5→81.613 Å / Num. obs: 166081 / % possible obs: 99.7 % / Redundancy: 1.9 % / CC1/2: 0.996 / Net I/σ(I): 7
Reflection shellResolution: 1.5→1.53 Å / Mean I/σ(I) obs: 1.5 / Num. unique obs: 8213 / CC1/2: 0.577

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7AN1

7an1


Resolution: 1.5→81.613 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.966 / WRfactor Rfree: 0.179 / WRfactor Rwork: 0.144 / SU B: 3.784 / SU ML: 0.058 / Average fsc free: 0.9439 / Average fsc work: 0.9534 / Cross valid method: FREE R-VALUE / ESU R: 0.071 / ESU R Free: 0.063
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1757 8251 4.975 %
Rwork0.1415 157595 -
all0.143 --
obs-165846 99.473 %
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: 17.155 Å2
Baniso -1Baniso -2Baniso -3
1--0.453 Å20 Å2-0.318 Å2
2--2.979 Å2-0 Å2
3----1.708 Å2
Refinement stepCycle: LAST / Resolution: 1.5→81.613 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7625 0 83 755 8463
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0138099
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177310
X-RAY DIFFRACTIONr_angle_refined_deg1.4771.64811034
X-RAY DIFFRACTIONr_angle_other_deg1.4091.58316923
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.62151009
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.75823.673392
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.701151293
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2351529
X-RAY DIFFRACTIONr_chiral_restr0.0780.21047
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.029282
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021828
X-RAY DIFFRACTIONr_nbd_refined0.1990.21630
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1830.27017
X-RAY DIFFRACTIONr_nbtor_refined0.1680.23890
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.23297
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1180.2590
X-RAY DIFFRACTIONr_metal_ion_refined0.1230.27
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2130.219
X-RAY DIFFRACTIONr_nbd_other0.220.260
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1780.230
X-RAY DIFFRACTIONr_mcbond_it1.7531.6413991
X-RAY DIFFRACTIONr_mcbond_other1.7451.6413990
X-RAY DIFFRACTIONr_mcangle_it2.1832.4815015
X-RAY DIFFRACTIONr_mcangle_other2.1832.4825016
X-RAY DIFFRACTIONr_scbond_it2.291.8654108
X-RAY DIFFRACTIONr_scbond_other2.2911.8654105
X-RAY DIFFRACTIONr_scangle_it2.7582.7156019
X-RAY DIFFRACTIONr_scangle_other2.7592.7156017
X-RAY DIFFRACTIONr_lrange_it3.08320.4619370
X-RAY DIFFRACTIONr_lrange_other2.88120.0049204
X-RAY DIFFRACTIONr_rigid_bond_restr8.597315407
X-RAY DIFFRACTIONr_ncsr_local_group_10.0580.0516999
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AAAX-RAY DIFFRACTIONLocal ncs0.057790.05009
12CCCX-RAY DIFFRACTIONLocal ncs0.057790.05009
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.5390.3225590.26911658X-RAY DIFFRACTION99.2606
1.539-1.5810.2645880.23611275X-RAY DIFFRACTION99.3718
1.581-1.6270.2495690.21611049X-RAY DIFFRACTION99.2228
1.627-1.6770.2295190.18110674X-RAY DIFFRACTION99.4933
1.677-1.7320.2165650.16510357X-RAY DIFFRACTION99.7534
1.732-1.7930.1945100.15210125X-RAY DIFFRACTION99.8592
1.793-1.860.1875150.1349715X-RAY DIFFRACTION99.8341
1.86-1.9360.1775030.139344X-RAY DIFFRACTION99.8074
1.936-2.0220.1734620.138985X-RAY DIFFRACTION99.5889
2.022-2.1210.1634360.138567X-RAY DIFFRACTION99.7341
2.121-2.2360.1674740.1288115X-RAY DIFFRACTION99.7793
2.236-2.3710.1684210.1197680X-RAY DIFFRACTION99.6678
2.371-2.5350.1473900.117256X-RAY DIFFRACTION99.6741
2.535-2.7380.153950.1146685X-RAY DIFFRACTION99.1319
2.738-2.9990.1733290.1286167X-RAY DIFFRACTION99.1604
2.999-3.3520.162640.1365652X-RAY DIFFRACTION99.1785
3.352-3.870.1522390.1284991X-RAY DIFFRACTION99.1093
3.87-4.7370.1382280.1194178X-RAY DIFFRACTION98.8114
4.737-6.690.1821900.1713275X-RAY DIFFRACTION99.4832
6.69-81.6130.224950.1981847X-RAY DIFFRACTION99.335

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