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- PDB-7p26: Sulfated host glycan recognition by carbohydrate sulfatases of th... -

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Basic information

Entry
Database: PDB / ID: 7p26
TitleSulfated host glycan recognition by carbohydrate sulfatases of the human gut microbiota (BT4631_S1_15)
ComponentsPutative arylsulfatase
KeywordsHYDROLASE / Host glycans / sulfation / carbohydrate sulfatases / microbiota
Function / homology
Function and homology information


sulfuric ester hydrolase activity
Similarity search - Function
: / : / Sulfatases signature 1. / Sulfatase, conserved site / Sulfatase, N-terminal / Sulfatase / Alkaline-phosphatase-like, core domain superfamily
Similarity search - Domain/homology
polyethylene glycol / Putative arylsulfatase
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 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 4, 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: Putative arylsulfatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,5326
Polymers57,2541
Non-polymers2,2795
Water10,791599
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area260 Å2
ΔGint-18 kcal/mol
Surface area18220 Å2
Unit cell
Length a, b, c (Å)49.924, 109.572, 117.531
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11AAA-1077-

HOH

21AAA-1124-

HOH

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Components

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Protein , 1 types, 1 molecules AAA

#1: Protein Putative arylsulfatase /


Mass: 57253.625 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_4631
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q89YV0

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Non-polymers , 5 types, 604 molecules

#2: 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
#3: Chemical ChemComp-P4K / polyethylene glycol / 3,6,9,12,15,18,21,24,27,30,33,36,39,42-tetradecaoxatetratetracontan-1-ol / Polyethylene glycol


Mass: 662.804 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H62O15
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 599 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.81 Å3/Da / Density % sol: 56.19 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 80 mg/ml BT4631 with 10 mM 6S-Gal was crystallised in 20 % PEG 10K and 0.1 M Bicine pH8.5.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9786 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.35→109.57 Å / Num. obs: 140145 / % possible obs: 98.8 % / Redundancy: 12.4 % / CC1/2: 0.999 / Net I/σ(I): 25.4
Reflection shellResolution: 1.35→1.37 Å / Mean I/σ(I) obs: 4.5 / Num. unique obs: 6050 / CC1/2: 0.955

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Processing

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

7oze


Resolution: 1.35→80.274 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.971 / WRfactor Rfree: 0.139 / WRfactor Rwork: 0.123 / SU B: 1.011 / SU ML: 0.019 / Average fsc free: 0.9798 / Average fsc work: 0.9824 / Cross valid method: FREE R-VALUE / ESU R: 0.039 / ESU R Free: 0.036
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1391 7206 5.145 %
Rwork0.1233 132849 -
all0.124 --
obs-140055 98.612 %
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: 14.129 Å2
Baniso -1Baniso -2Baniso -3
1-0.928 Å2-0 Å20 Å2
2---0.247 Å2-0 Å2
3----0.681 Å2
Refinement stepCycle: LAST / Resolution: 1.35→80.274 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3780 0 31 599 4410
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0134217
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173940
X-RAY DIFFRACTIONr_angle_refined_deg1.4821.6475759
X-RAY DIFFRACTIONr_angle_other_deg1.4741.5849146
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8695552
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.77422.573206
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.54315713
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3931524
X-RAY DIFFRACTIONr_chiral_restr0.0780.2549
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024938
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02966
X-RAY DIFFRACTIONr_nbd_refined0.2380.2833
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1820.23631
X-RAY DIFFRACTIONr_nbtor_refined0.170.21990
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.21740
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.2430
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0140.22
X-RAY DIFFRACTIONr_metal_ion_refined0.1110.29
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.4280.26
X-RAY DIFFRACTIONr_nbd_other0.3020.232
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.190.215
X-RAY DIFFRACTIONr_mcbond_it0.9811.2142111
X-RAY DIFFRACTIONr_mcbond_other0.9311.2112109
X-RAY DIFFRACTIONr_mcangle_it1.1761.8322694
X-RAY DIFFRACTIONr_mcangle_other1.1751.8322694
X-RAY DIFFRACTIONr_scbond_it1.3741.4842106
X-RAY DIFFRACTIONr_scbond_other1.3741.4852107
X-RAY DIFFRACTIONr_scangle_it1.6392.1043065
X-RAY DIFFRACTIONr_scangle_other1.6392.1053066
X-RAY DIFFRACTIONr_lrange_it2.71916.3414963
X-RAY DIFFRACTIONr_lrange_other2.21315.4754810
X-RAY DIFFRACTIONr_rigid_bond_restr1.20238155
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.3850.1614580.1448795X-RAY DIFFRACTION89.0139
1.385-1.4230.1385140.1219226X-RAY DIFFRACTION96.2641
1.423-1.4640.1245040.1079178X-RAY DIFFRACTION98.3244
1.464-1.5090.1234920.1029006X-RAY DIFFRACTION99.258
1.509-1.5590.1224990.0948792X-RAY DIFFRACTION99.5287
1.559-1.6130.1184550.098481X-RAY DIFFRACTION99.4768
1.613-1.6740.1074320.0878212X-RAY DIFFRACTION99.6656
1.674-1.7430.1083920.0917943X-RAY DIFFRACTION99.7487
1.743-1.820.1133880.0967619X-RAY DIFFRACTION99.8379
1.82-1.9090.1243890.1057338X-RAY DIFFRACTION99.9483
1.909-2.0120.1213750.1146936X-RAY DIFFRACTION99.9727
2.012-2.1340.1353490.1196586X-RAY DIFFRACTION99.9856
2.134-2.2820.1243500.1156224X-RAY DIFFRACTION99.9848
2.282-2.4640.1353650.1115734X-RAY DIFFRACTION99.9836
2.464-2.6990.1222990.1145331X-RAY DIFFRACTION100
2.699-3.0180.1572740.1324848X-RAY DIFFRACTION99.9805
3.018-3.4840.1722570.1484290X-RAY DIFFRACTION99.978
3.484-4.2660.1531810.143701X-RAY DIFFRACTION100
4.266-6.030.1861470.1722920X-RAY DIFFRACTION100
6.03-80.2740.201860.211689X-RAY DIFFRACTION99.2174

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