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- PDB-7p24: Sulfated host glycan recognition by carbohydrate sulfatases of th... -

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Basic information

Entry
Database: PDB / ID: 7p24
TitleSulfated host glycan recognition by carbohydrate sulfatases of the human gut microbiota (BT3177_S1_11)
ComponentsMucin-desulfating sulfatase
KeywordsHYDROLASE / Host glycans / sulfation / carbohydrate sulfatases / microbiota
Function / homology
Function and homology information


sulfuric ester hydrolase activity
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
Chem-NGS / Chem-NGY / Mucin-desulfating sulfatase
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.97 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
DepositionJul 3, 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: Mucin-desulfating sulfatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,6814
Polymers61,0381
Non-polymers6433
Water10,683593
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area490 Å2
ΔGint-0 kcal/mol
Surface area18730 Å2
Unit cell
Length a, b, c (Å)42.129, 69.780, 96.286
Angle α, β, γ (deg.)90.000, 97.644, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Mucin-desulfating sulfatase


Mass: 61037.914 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_3177
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q8A2X8
#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: Sugar ChemComp-NGY / 2-acetamido-2-deoxy-6-O-sulfo-alpha-D-glucopyranose / 2-(acetylamino)-2-deoxy-6-O-sulfo-alpha-D-glucopyranose / N-acetyl-6-O-sulfo-alpha-D-glucosamine / 2-acetamido-2-deoxy-6-O-sulfo-alpha-D-glucose / 2-acetamido-2-deoxy-6-O-sulfo-D-glucose / 2-acetamido-2-deoxy-6-O-sulfo-glucose


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


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 593 / 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: 2.3 Å3/Da / Density % sol: 46.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20 mg/ml BT3177S1_11 with 10 mM 6S-GlcNAc crystallised in 50 % precipitant mix 1 (40% v/v PEG 500, MME; 20 % w/v PEG 20000), 0.1 M carboxcylic acids (0.2M Sodium formate; 0.2M Ammonium ...Details: 20 mg/ml BT3177S1_11 with 10 mM 6S-GlcNAc crystallised in 50 % precipitant mix 1 (40% v/v PEG 500, MME; 20 % w/v PEG 20000), 0.1 M carboxcylic acids (0.2M Sodium formate; 0.2M Ammonium acetate; 0.2M Sodium citrate tribasic dihydrate; 0.2M Sodium potassium tartrate tetrahydrate; 0.2M Sodium oxamate) and 0.1 M buffer system 3 pH 8.5 (Tris (base); BICINE).

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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: 0.97→35.856 Å / Num. obs: 298423 / % possible obs: 91.9 % / Redundancy: 1.9 % / CC1/2: 0.996 / Net I/σ(I): 8.8
Reflection shellResolution: 0.97→0.99 Å / Mean I/σ(I) obs: 1.5 / Num. unique obs: 12666 / CC1/2: 0.596

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5G2V

5g2v


Resolution: 0.97→35.856 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.981 / WRfactor Rfree: 0.141 / WRfactor Rwork: 0.126 / SU B: 0.705 / SU ML: 0.016 / Average fsc free: 0.9606 / Average fsc work: 0.9634 / Cross valid method: FREE R-VALUE / ESU R: 0.018 / ESU R Free: 0.019
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1362 14930 5.004 %
Rwork0.1236 283440 -
all0.124 --
obs-298370 91.71 %
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: 11.374 Å2
Baniso -1Baniso -2Baniso -3
1-1.281 Å2-0 Å20.725 Å2
2--0.419 Å2-0 Å2
3----1.829 Å2
Refinement stepCycle: LAST / Resolution: 0.97→35.856 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4110 0 39 593 4742
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0134674
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174239
X-RAY DIFFRACTIONr_angle_refined_deg1.5021.6556384
X-RAY DIFFRACTIONr_angle_other_deg1.5031.5889828
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2215577
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.36722.338278
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.36715820
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.9231531
X-RAY DIFFRACTIONr_chiral_restr0.0830.2577
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025495
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021151
X-RAY DIFFRACTIONr_nbd_refined0.2470.2995
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1810.24040
X-RAY DIFFRACTIONr_nbtor_refined0.180.22194
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.21909
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2458
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0740.22
X-RAY DIFFRACTIONr_metal_ion_refined0.0480.25
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1990.26
X-RAY DIFFRACTIONr_nbd_other0.220.243
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1290.228
X-RAY DIFFRACTIONr_mcbond_it0.7911.0112191
X-RAY DIFFRACTIONr_mcbond_other0.7881.012190
X-RAY DIFFRACTIONr_mcangle_it1.021.5242807
X-RAY DIFFRACTIONr_mcangle_other1.021.5252808
X-RAY DIFFRACTIONr_scbond_it0.8911.1642483
X-RAY DIFFRACTIONr_scbond_other0.8921.1652478
X-RAY DIFFRACTIONr_scangle_it1.1411.6943577
X-RAY DIFFRACTIONr_scangle_other1.1421.6953572
X-RAY DIFFRACTIONr_lrange_it2.13513.1015629
X-RAY DIFFRACTIONr_lrange_other1.75312.2665440
X-RAY DIFFRACTIONr_rigid_bond_restr3.138913
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.97-0.9950.2539620.24318004X-RAY DIFFRACTION79.1008
0.995-1.0220.2219320.2117605X-RAY DIFFRACTION79.2179
1.022-1.0520.19410390.18719491X-RAY DIFFRACTION90.1427
1.052-1.0840.1710330.16218956X-RAY DIFFRACTION90.5012
1.084-1.120.15510110.13718500X-RAY DIFFRACTION91.2795
1.12-1.1590.1349260.12718114X-RAY DIFFRACTION91.9229
1.159-1.2030.1389300.12217644X-RAY DIFFRACTION92.5046
1.203-1.2520.1299660.11616883X-RAY DIFFRACTION93.0314
1.252-1.3080.1248480.10816421X-RAY DIFFRACTION93.5685
1.308-1.3720.127960.10215802X-RAY DIFFRACTION93.9332
1.372-1.4460.1157940.09515141X-RAY DIFFRACTION94.7497
1.446-1.5340.1057290.09314433X-RAY DIFFRACTION95.2686
1.534-1.6390.1126850.09213639X-RAY DIFFRACTION95.9603
1.639-1.7710.1116740.09612774X-RAY DIFFRACTION96.4775
1.771-1.940.1215670.10511841X-RAY DIFFRACTION96.7485
1.94-2.1690.1275100.11110808X-RAY DIFFRACTION97.4765
2.169-2.5040.1255180.1149520X-RAY DIFFRACTION97.8458
2.504-3.0660.1454620.1318048X-RAY DIFFRACTION98.0189
3.066-4.3340.1353510.1366314X-RAY DIFFRACTION98.6093
4.334-35.8560.171970.1673502X-RAY DIFFRACTION97.9349

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