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- PDB-6s20: Metabolism of multiple glycosaminoglycans by bacteroides thetaiot... -

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Basic information

Entry
Database: PDB / ID: 6s20
TitleMetabolism of multiple glycosaminoglycans by bacteroides thetaiotaomicron is orchestrated by a versatile core genetic locus (BT33336S-sulf)
ComponentsN-acetylgalactosamine-6-O-sulfatase
KeywordsHYDROLASE / Gut microbiota / Glycosaminoglycan / Glycobiology / CAZymes
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Sulfuric-ester hydrolases / hydrolase activity
Similarity search - Function
: / : / Sulfatases signature 2. / Sulfatases signature 1. / Sulfatase, conserved site / Sulfatase, N-terminal / Sulfatase / Alkaline-phosphatase-like, core domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Chem-NG6 / TRIETHYLENE GLYCOL / N-acetylgalactosamine-6-O-sulfatase
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsNdeh, D. / Basle, A. / Strahl, H. / Henrissat, B. / Terrapon, N. / Cartmell, A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
European Research Council322820 United Kingdom
CitationJournal: Nat Commun / Year: 2020
Title: Metabolism of multiple glycosaminoglycans by Bacteroides thetaiotaomicron is orchestrated by a versatile core genetic locus.
Authors: Ndeh, D. / Basle, A. / Strahl, H. / Yates, E.A. / McClurgg, U.L. / Henrissat, B. / Terrapon, N. / Cartmell, A.
History
DepositionJun 19, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 5, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 20, 2020Group: Structure summary / Category: struct / Item: _struct.title
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1May 15, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: N-acetylgalactosamine-6-O-sulfatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1274
Polymers56,6351
Non-polymers4923
Water2,018112
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area860 Å2
ΔGint-6 kcal/mol
Surface area16980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.400, 86.400, 122.210
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein N-acetylgalactosamine-6-O-sulfatase


Mass: 56635.367 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_3333 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8A2H2, Hydrolases; Acting on ester bonds; Sulfuric-ester hydrolases
#2: Sugar ChemComp-NG6 / 2-acetamido-2-deoxy-6-O-sulfo-beta-D-galactopyranose / N-ACETYL-D-GALACTOSAMINE 6-SULFATE / N-acetyl-6-O-sulfo-beta-D-galactosamine / 2-acetamido-2-deoxy-6-O-sulfo-beta-D-galactose / 2-acetamido-2-deoxy-6-O-sulfo-D-galactose / 2-acetamido-2-deoxy-6-O-sulfo-galactose


Type: D-saccharide, beta linking / Mass: 301.271 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO9S / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGalpNAc[6S]bCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-6-sulfo-b-D-galactopyranoseCOMMON NAMEGMML 1.0
b-D-GalpNAc6SO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#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


Mass: 18.015 Da / Num. of mol.: 112 / 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: 2.01 Å3/Da / Density % sol: 38.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 30 % PEG 4000, 200 mM MgCl2, and 0.1 M Tris, pH 8.5. 20m/gml protein and 10 mM GlaNAc6S

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Data collection

DiffractionMean temperature: 173 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.98→70.65 Å / Num. obs: 32979 / % possible obs: 100 % / Redundancy: 14.2 % / CC1/2: 0.998 / Net I/σ(I): 11
Reflection shellResolution: 1.98→2.03 Å / Num. unique obs: 2253 / CC1/2: 0.561

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.98→70.65 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.94 / SU B: 4.396 / SU ML: 0.12 / Cross valid method: THROUGHOUT / ESU R: 0.176 / ESU R Free: 0.156 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22364 1396 4.2 %RANDOM
Rwork0.1805 ---
obs0.18249 31519 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 28.89 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å20 Å2
2---0.08 Å20 Å2
3---0.16 Å2
Refinement stepCycle: 1 / Resolution: 1.98→70.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3664 0 29 112 3805
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0133800
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173384
X-RAY DIFFRACTIONr_angle_refined_deg1.5311.655195
X-RAY DIFFRACTIONr_angle_other_deg1.3441.5747862
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5115483
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.88923.462182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.67215566
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9831516
X-RAY DIFFRACTIONr_chiral_restr0.0690.2513
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024312
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02761
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0473.0241929
X-RAY DIFFRACTIONr_mcbond_other2.0433.0221928
X-RAY DIFFRACTIONr_mcangle_it2.8454.5262413
X-RAY DIFFRACTIONr_mcangle_other2.8444.5282414
X-RAY DIFFRACTIONr_scbond_it2.7473.2711869
X-RAY DIFFRACTIONr_scbond_other2.7483.2751870
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.9844.8082780
X-RAY DIFFRACTIONr_long_range_B_refined5.11836.1884213
X-RAY DIFFRACTIONr_long_range_B_other5.17836.194206
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.98→2.031 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork0.253 2378 -
obs--100 %

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