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- PDB-7oz9: Sulfated host glycan recognition by carbohydrate sulfatases of th... -

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Basic information

Entry
Database: PDB / ID: 7oz9
TitleSulfated host glycan recognition by carbohydrate sulfatases of the human gut microbiota (BT3057-S1_16)
ComponentsN-acetylgalactosamine-6-sulfatase
KeywordsHYDROLASE / Sulfatase / Host glycans / microbiota / carbohydrate
Function / homology
Function and homology information


arylsulfatase activity / metal ion binding
Similarity search - Function
: / Sulfatases signature 1. / Sulfatase, conserved site / Sulfatase, N-terminal / Sulfatase / Alkaline-phosphatase-like, core domain superfamily
Similarity search - Domain/homology
Chem-ASG / Chem-NGK / N-acetylgalactosamine-6-sulfatase
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.907 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: N-acetylgalactosamine-6-sulfatase
BBB: N-acetylgalactosamine-6-sulfatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,3428
Polymers114,0572
Non-polymers1,2856
Water7,296405
1
AAA: N-acetylgalactosamine-6-sulfatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6714
Polymers57,0281
Non-polymers6433
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: N-acetylgalactosamine-6-sulfatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6714
Polymers57,0281
Non-polymers6433
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.170, 90.755, 94.169
Angle α, β, γ (deg.)90.000, 98.550, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein N-acetylgalactosamine-6-sulfatase


Mass: 57028.387 Da / Num. of mol.: 2
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_3057
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q8A397
#2: Sugar ChemComp-ASG / 2-acetamido-2-deoxy-4-O-sulfo-beta-D-galactopyranose / 2-DEOXY-2-ACETAMIDO-BETA-D-GALACTOSE-4-SULFATE / N-acetyl-4-O-sulfo-beta-D-galactosamine / 2-acetamido-2-deoxy-4-O-sulfo-beta-D-galactose / 2-acetamido-2-deoxy-4-O-sulfo-D-galactose / 2-acetamido-2-deoxy-4-O-sulfo-galactose


Type: D-saccharide, beta linking / Mass: 301.271 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO9S / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGalpNAc[4S]bCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-4-sulfo-b-D-galactopyranoseCOMMON NAMEGMML 1.0
b-D-GalpNAc4SO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Sugar ChemComp-NGK / 2-acetamido-2-deoxy-4-O-sulfo-alpha-D-galactopyranose / 2-(ACETYLAMINO)-2-DEOXY-4-O-SULFO-ALPHA-D-GALACTOPYRANOSE / N-acetyl-4-O-sulfo-alpha-D-galactosamine / 2-acetamido-2-deoxy-4-O-sulfo-alpha-D-galactose / 2-acetamido-2-deoxy-4-O-sulfo-D-galactose / 2-acetamido-2-deoxy-4-O-sulfo-galactose


Type: D-saccharide, alpha linking / Mass: 301.271 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO9S / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGalpNAc[4S]aCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-4-sulfo-a-D-galactopyranoseCOMMON NAMEGMML 1.0
a-D-GalpNAc4SO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 405 / 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: 2.45 Å3/Da / Density % sol: 49.83 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 35 mg/ml BT3057S1_16 with 10 mM 4S-GalNAc was crystallised in 20 % PEG 3350 and 0.2 M sodium nitrate

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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: 1.907→65.52 Å / Num. obs: 85409 / % possible obs: 99.6 % / Redundancy: 1.9 % / CC1/2: 0.992 / Net I/σ(I): 8.8
Reflection shellResolution: 1.91→1.94 Å / Mean I/σ(I) obs: 2.2 / Num. unique obs: 4269 / CC1/2: 0.39

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Processing

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

7an1


Resolution: 1.907→65.52 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.932 / WRfactor Rfree: 0.223 / WRfactor Rwork: 0.183 / SU B: 3.73 / SU ML: 0.105 / Average fsc free: 0.9126 / Average fsc work: 0.9213 / Cross valid method: FREE R-VALUE / ESU R: 0.146 / ESU R Free: 0.137
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2233 4097 4.797 %
Rwork0.1849 81311 -
all0.187 --
obs-85408 99.594 %
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: 23.895 Å2
Baniso -1Baniso -2Baniso -3
1-0.256 Å20 Å2-0.004 Å2
2--0.587 Å2-0 Å2
3----0.805 Å2
Refinement stepCycle: LAST / Resolution: 1.907→65.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7540 0 78 405 8023
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0137868
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177173
X-RAY DIFFRACTIONr_angle_refined_deg1.4781.65510682
X-RAY DIFFRACTIONr_angle_other_deg1.2811.57916558
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.145973
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.52822.09421
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.12151263
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6511550
X-RAY DIFFRACTIONr_chiral_restr0.0690.21000
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.029022
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021834
X-RAY DIFFRACTIONr_nbd_refined0.1950.21571
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1780.26840
X-RAY DIFFRACTIONr_nbtor_refined0.1630.23734
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0750.23437
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2438
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0930.22
X-RAY DIFFRACTIONr_metal_ion_refined0.1450.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1140.213
X-RAY DIFFRACTIONr_nbd_other0.1420.243
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0870.210
X-RAY DIFFRACTIONr_mcbond_it1.6222.4533883
X-RAY DIFFRACTIONr_mcbond_other1.6212.4523882
X-RAY DIFFRACTIONr_mcangle_it2.353.6724859
X-RAY DIFFRACTIONr_mcangle_other2.353.6734860
X-RAY DIFFRACTIONr_scbond_it1.9382.6173985
X-RAY DIFFRACTIONr_scbond_other1.9382.6183980
X-RAY DIFFRACTIONr_scangle_it2.9963.855823
X-RAY DIFFRACTIONr_scangle_other2.9963.8515818
X-RAY DIFFRACTIONr_lrange_it4.16928.5848737
X-RAY DIFFRACTIONr_lrange_other4.1328.4868666
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.907-1.9570.2853130.2655753X-RAY DIFFRACTION96.1636
1.957-2.0110.2623070.2485864X-RAY DIFFRACTION99.8544
2.011-2.0690.2632510.2385726X-RAY DIFFRACTION99.7663
2.069-2.1320.2492680.2215522X-RAY DIFFRACTION99.9482
2.132-2.2020.2612660.2185373X-RAY DIFFRACTION99.9291
2.202-2.280.2662530.2065193X-RAY DIFFRACTION99.9083
2.28-2.3660.2252640.1934991X-RAY DIFFRACTION99.9049
2.366-2.4620.2272530.1824811X-RAY DIFFRACTION99.7439
2.462-2.5710.2312470.1824574X-RAY DIFFRACTION99.8343
2.571-2.6970.2252220.1814444X-RAY DIFFRACTION99.9572
2.697-2.8430.2212080.1774227X-RAY DIFFRACTION99.9549
2.843-3.0150.2272130.1913991X-RAY DIFFRACTION100
3.015-3.2230.2311870.1923731X-RAY DIFFRACTION99.9745
3.223-3.4810.2351780.1923512X-RAY DIFFRACTION99.9188
3.481-3.8120.2091570.1783201X-RAY DIFFRACTION99.9107
3.812-4.2610.171540.1442929X-RAY DIFFRACTION99.9352
4.261-4.9190.1761140.132582X-RAY DIFFRACTION99.9629
4.919-6.020.166980.1472219X-RAY DIFFRACTION100
6.02-8.4960.238930.1721698X-RAY DIFFRACTION100
8.496-65.520.196510.164971X-RAY DIFFRACTION100

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