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- PDB-7anb: A single sulfatase is required for metabolism of colonic mucin O-... -

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Basic information

Entry
Database: PDB / ID: 7anb
TitleA single sulfatase is required for metabolism of colonic mucin O-glycans and intestinal colonization by a symbiotic human gut bacterium (BT1622-S1_20)
ComponentsN-acetylgalactosamine-6-sulfatase
KeywordsHYDROLASE / Carbohydrate sulfatase / mucin / microbiome / bacteroides
Function / homologySulfatases signature 1. / Sulfatase, conserved site / sulfuric ester hydrolase activity / Sulfatase, N-terminal / Sulfatase / Alkaline-phosphatase-like, core domain superfamily / N-acetylgalactosamine-6-sulfatase
Function and homology information
Biological speciesBacteroides thetaiotaomicron VPI-5482 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsSofia de Jesus Vaz Luis, A. / Basle, A. / Martens, E.C. / Cartmell, A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome TrustSBF0051065163470 United Kingdom
CitationJournal: Nature / Year: 2021
Title: A single sulfatase is required to access colonic mucin by a gut bacterium.
Authors: Luis, A.S. / Jin, C. / Pereira, G.V. / Glowacki, R.W.P. / Gugel, S.R. / Singh, S. / Byrne, D.P. / Pudlo, N.A. / London, J.A. / Basle, A. / Reihill, M. / Oscarson, S. / Eyers, P.A. / Czjzek, ...Authors: Luis, A.S. / Jin, C. / Pereira, G.V. / Glowacki, R.W.P. / Gugel, S.R. / Singh, S. / Byrne, D.P. / Pudlo, N.A. / London, J.A. / Basle, A. / Reihill, M. / Oscarson, S. / Eyers, P.A. / Czjzek, M. / Michel, G. / Barbeyron, T. / Yates, E.A. / Hansson, G.C. / Karlsson, N.G. / Cartmell, A. / Martens, E.C.
History
DepositionOct 11, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 27, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 3, 2021Group: Data collection / Category: pdbx_database_proc
Revision 1.2May 1, 2024Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _diffrn_source.pdbx_synchrotron_site / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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)114,1109
Polymers113,6522
Non-polymers4587
Water52229
1
AAA: N-acetylgalactosamine-6-sulfatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,0865
Polymers56,8261
Non-polymers2604
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: N-acetylgalactosamine-6-sulfatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,0244
Polymers56,8261
Non-polymers1983
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.268, 81.268, 383.735
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11AAA
21BBB

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: PHE / End label comp-ID: PHE / Auth seq-ID: 26 - 500 / Label seq-ID: 29 - 503

Dom-IDComponent-IDAuth asym-IDLabel asym-ID
11AAAA
22BBBB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

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


Mass: 56825.832 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron VPI-5482 (bacteria)
Gene: BT_1622 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8A7A3
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 29 / Source method: isolated from a natural source / Formula: H2O
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: 2.79 Å3/Da / Density % sol: 55.87 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 20 % PEG 3350, 0.2 M Sodium citrate, 25 mg/ml BT1622 and 10 mM LacNAc.

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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 XE 16M / Detector: PIXEL / Date: Jul 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.6→96.118 Å / Num. obs: 40144 / % possible obs: 97.8 % / Redundancy: 7.3 % / CC1/2: 0.987 / Net I/σ(I): 5.5
Reflection shellResolution: 2.6→2.71 Å / Num. unique obs: 4376 / CC1/2: 0.344

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: BT1624

Resolution: 2.6→95.93 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.923 / SU B: 32.844 / SU ML: 0.284 / Cross valid method: FREE R-VALUE / ESU R: 0.586 / ESU R Free: 0.292
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2448 1975 4.936 %
Rwork0.2187 38040 -
all0.22 --
obs-40015 97.614 %
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: 57.279 Å2
Baniso -1Baniso -2Baniso -3
1-0.003 Å20 Å20 Å2
2--0.003 Å20 Å2
3----0.007 Å2
Refinement stepCycle: LAST / Resolution: 2.6→95.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7570 0 24 29 7623
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0137815
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177049
X-RAY DIFFRACTIONr_angle_refined_deg1.3191.65410600
X-RAY DIFFRACTIONr_angle_other_deg1.1291.5816297
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3985948
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.25822.736424
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.265151244
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0371540
X-RAY DIFFRACTIONr_chiral_restr0.0540.2968
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.028986
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021862
X-RAY DIFFRACTIONr_nbd_refined0.1890.21577
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1760.26799
X-RAY DIFFRACTIONr_nbtor_refined0.1640.23701
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0740.23356
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2171
X-RAY DIFFRACTIONr_metal_ion_refined0.1790.27
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1550.28
X-RAY DIFFRACTIONr_nbd_other0.1710.233
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1260.25
X-RAY DIFFRACTIONr_mcbond_it0.3792.1333798
X-RAY DIFFRACTIONr_mcbond_other0.3792.1323797
X-RAY DIFFRACTIONr_mcangle_it0.6723.1984744
X-RAY DIFFRACTIONr_mcangle_other0.6723.1994745
X-RAY DIFFRACTIONr_scbond_it0.322.1664017
X-RAY DIFFRACTIONr_scbond_other0.322.1664018
X-RAY DIFFRACTIONr_scangle_it0.5723.235856
X-RAY DIFFRACTIONr_scangle_other0.5723.2315857
X-RAY DIFFRACTIONr_lrange_it1.87924.4268578
X-RAY DIFFRACTIONr_lrange_other1.87524.4228578
X-RAY DIFFRACTIONr_ncsr_local_group_10.0490.0516425
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AAAX-RAY DIFFRACTIONLocal ncs0.048750.0501
12BBBX-RAY DIFFRACTIONLocal ncs0.048750.0501
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.6670.3581430.382700X-RAY DIFFRACTION96.3402
2.667-2.7410.3951510.3622614X-RAY DIFFRACTION95.148
2.741-2.820.3981290.3352602X-RAY DIFFRACTION97.3966
2.82-2.9070.3141250.3122520X-RAY DIFFRACTION96.4976
2.907-3.0020.2941400.3032394X-RAY DIFFRACTION96.0576
3.002-3.1070.3091200.2822343X-RAY DIFFRACTION95.4651
3.107-3.2250.3521160.2572281X-RAY DIFFRACTION96.42
3.225-3.3560.2591120.2462175X-RAY DIFFRACTION95.6104
3.356-3.5060.2511160.2182128X-RAY DIFFRACTION96.6408
3.506-3.6770.2351110.22061X-RAY DIFFRACTION98.2805
3.677-3.8760.231020.1942018X-RAY DIFFRACTION99.6241
3.876-4.1110.1921250.1811869X-RAY DIFFRACTION99.8498
4.111-4.3940.194920.1691785X-RAY DIFFRACTION100
4.394-4.7470.159850.1461699X-RAY DIFFRACTION99.888
4.747-5.1990.192730.1611581X-RAY DIFFRACTION100
5.199-5.8130.22720.1791441X-RAY DIFFRACTION100
5.813-6.7120.233530.1861284X-RAY DIFFRACTION100
6.712-8.220.211460.1861119X-RAY DIFFRACTION100
8.22-11.6220.194420.166883X-RAY DIFFRACTION100
11.622-95.930.25220.292543X-RAY DIFFRACTION99.4718
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.27760.38991.21071.15030.12012.11680.05830.3512-0.1817-0.15170.0428-0.2030.12490.3457-0.10110.52060.0684-0.02830.52840.00670.09411.5657-28.6424-0.2226
22.05030.2655-0.59412.2466-0.43731.5135-0.00010.0029-0.05390.05090.10320.0259-0.1456-0.0894-0.10310.42350.0237-0.05590.33650.00680.0233-24.1615-28.3352-38.2511
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLAAA26 - 500
2X-RAY DIFFRACTION1ALLAAA601
3X-RAY DIFFRACTION1ALLAAA602
4X-RAY DIFFRACTION2ALLBBB26 - 500
5X-RAY DIFFRACTION2ALLBBB601

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