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- PDB-7oz8: Sulfated host glycan recognition by carbohydrate sulfatases of th... -

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Basic information

Entry
Database: PDB / ID: 7oz8
TitleSulfated host glycan recognition by carbohydrate sulfatases of the human gut microbiota (BT1918_S1_46)
ComponentsCholine-sulfatase
KeywordsHYDROLASE / Host glycans / sulfation / carbohydrate sulfatases / microbiota
Function / homology
Function and homology information


arylsulfatase activity
Similarity search - Function
Sulfatases signature 2. / Sulfatases signature 1. / Sulfatase, conserved site / Sulfatase, N-terminal / Sulfatase / Alkaline-phosphatase-like, core domain superfamily
Similarity search - Domain/homology
ACETATE ION / Chem-NGS / Choline-sulfatase
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron VPI-5482 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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 / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Choline-sulfatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,8813
Polymers57,5211
Non-polymers3602
Water3,009167
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering, Dimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area780 Å2
ΔGint1 kcal/mol
Surface area17930 Å2
Unit cell
Length a, b, c (Å)56.389, 56.389, 279.763
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11AAA-719-

HOH

21AAA-803-

HOH

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Components

#1: Protein Choline-sulfatase


Mass: 57520.855 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron VPI-5482 (bacteria)
Gene: BT_1918
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q8A6G6
#2: Sugar ChemComp-NGS / 2-acetamido-2-deoxy-6-O-sulfo-beta-D-glucopyranose / 2-(acetylamino)-2-deoxy-6-O-sulfo-beta-D-glucopyranose / N-ACETYL-D-GLUCOSAMINE-6-SULFATE / N-acetyl-6-O-sulfo-beta-D-glucosamine / 2-acetamido-2-deoxy-6-O-sulfo-beta-D-glucose / 2-acetamido-2-deoxy-6-O-sulfo-D-glucose / 2-acetamido-2-deoxy-6-O-sulfo-glucose


Type: D-saccharide, beta linking / Mass: 301.271 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO9S / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAc[6S]bCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-6-sulfo-b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpNAc6SO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 2.23 Å3/Da / Density % sol: 44.9 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 20 mg/ml of BT1918S1_46 with 10 mM 6S-GlcNAc was crystallised in 45 % MPD, 0.2 M CaCl2 and 0.1 M Bis-Tris pH 5.5.

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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: Aug 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.95→48.153 Å / Num. obs: 39105 / % possible obs: 100 % / Redundancy: 10.3 % / CC1/2: 0.99 / Net I/σ(I): 5.8
Reflection shellResolution: 1.95→2 Å / Num. unique obs: 2675 / CC1/2: 0.803

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2vqr

2vqr


Resolution: 1.95→48.153 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.949 / WRfactor Rfree: 0.223 / WRfactor Rwork: 0.201 / SU B: 3.721 / SU ML: 0.101 / Average fsc free: 0.9255 / Average fsc work: 0.9304 / Cross valid method: FREE R-VALUE / ESU R: 0.163 / ESU R Free: 0.133
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2037 2032 5.21 %
Rwork0.1882 36971 -
all0.189 --
obs-39003 99.936 %
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: 29.506 Å2
Baniso -1Baniso -2Baniso -3
1-0.93 Å20.465 Å20 Å2
2--0.93 Å2-0 Å2
3----3.017 Å2
Refinement stepCycle: LAST / Resolution: 1.95→48.153 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3787 0 23 167 3977
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0133942
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173507
X-RAY DIFFRACTIONr_angle_refined_deg1.5111.6565361
X-RAY DIFFRACTIONr_angle_other_deg1.3211.5858108
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0825477
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.57222.714210
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.87515619
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2411519
X-RAY DIFFRACTIONr_chiral_restr0.0720.2490
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024512
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02923
X-RAY DIFFRACTIONr_nbd_refined0.2060.2780
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1890.23316
X-RAY DIFFRACTIONr_nbtor_refined0.1690.21880
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.21540
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.2198
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1890.212
X-RAY DIFFRACTIONr_nbd_other0.2050.247
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1610.24
X-RAY DIFFRACTIONr_mcbond_it2.113.0721906
X-RAY DIFFRACTIONr_mcbond_other2.113.0711904
X-RAY DIFFRACTIONr_mcangle_it2.8954.6022383
X-RAY DIFFRACTIONr_mcangle_other2.8954.6032384
X-RAY DIFFRACTIONr_scbond_it2.5153.232036
X-RAY DIFFRACTIONr_scbond_other2.5153.2292037
X-RAY DIFFRACTIONr_scangle_it3.8254.7652978
X-RAY DIFFRACTIONr_scangle_other3.8254.7642979
X-RAY DIFFRACTIONr_lrange_it4.84734.8264456
X-RAY DIFFRACTIONr_lrange_other4.84234.7894442
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.0010.3051340.2782670X-RAY DIFFRACTION99.822
2.001-2.0550.2461420.2552589X-RAY DIFFRACTION99.9268
2.055-2.1150.2561580.2282528X-RAY DIFFRACTION99.9256
2.115-2.180.2181490.2092475X-RAY DIFFRACTION100
2.18-2.2520.2251410.2032396X-RAY DIFFRACTION99.9606
2.252-2.3310.2131370.2032330X-RAY DIFFRACTION99.9595
2.331-2.4190.2341070.1862250X-RAY DIFFRACTION100
2.419-2.5170.2061150.182164X-RAY DIFFRACTION100
2.517-2.6290.192940.1812102X-RAY DIFFRACTION100
2.629-2.7580.2091390.181986X-RAY DIFFRACTION100
2.758-2.9070.2181000.1821904X-RAY DIFFRACTION99.9003
2.907-3.0830.213870.1951824X-RAY DIFFRACTION99.8955
3.083-3.2960.227900.2071732X-RAY DIFFRACTION100
3.296-3.560.166860.1931607X-RAY DIFFRACTION100
3.56-3.90.2051000.1861450X-RAY DIFFRACTION100
3.9-4.360.146590.1491376X-RAY DIFFRACTION100
4.36-5.0340.133620.1431210X-RAY DIFFRACTION100
5.034-6.1650.187520.1771058X-RAY DIFFRACTION100
6.165-8.7170.241560.177807X-RAY DIFFRACTION99.8843
8.717-48.1530.247240.195513X-RAY DIFFRACTION99.0775

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