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

ID or keywords:

Entry

Database: PDB / ID: 7ozc

Title

Sulfated host glycan recognition by carbohydrate sulfatases of the human gut microbiota (BT3109_S1_15)

Components

Arylsulfatase A

Keywords

HYDROLASE / Host glycans /

sulfation / carbohydrate sulfatases /

microbiota

Function / homology

Function and homology information

sulfuric ester hydrolase activity
Similarity search - Function

Biological species

Bacteroides thetaiotaomicron (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.75 Å

Authors

Cartmell, A.

Funding support

United Kingdom, 1items

Citation

Journal: 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

Deposition	Jun 27, 2021	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jun 29, 2022	Provider: repository / Type: Initial release
Revision 1.1	Aug 10, 2022	Group: 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 1.2	Jan 31, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7ozc.cif.gz	120.2 KB	Display	PDBx/mmCIF format
PDB format	pdb7ozc.ent.gz		Display	PDB format
PDBx/mmJSON format	7ozc.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/oz/7ozc ftp://data.pdbj.org/pub/pdb/validation_reports/oz/7ozc	HTTPS FTP

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Related structure data

Related structure data	7oz8C 7oz9C 7ozaC 7ozeC 7p24C 7p26C 6s20S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#50 - Feb 2004 Glycolytic Enzymes similarity (1)

Deposited unit

AAA: Arylsulfatase A

hetero molecules

57.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author
Evidence: light scattering

Unit cell

Length a, b, c (Å)	52.150, 91.760, 52.680
Angle α, β, γ (deg.)	90.000, 116.630, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein

Arylsulfatase A /

Mass: 57141.305 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_3109
Production host:

Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q8A346

#2: Sugar

ChemComp-G6S / 6-O-sulfo-beta-D-galactopyranose / D-GALACTOSE-6-SULFATE / 6-O-sulfo-beta-D-galactose / 6-O-sulfo-D-galactose / 6-O-sulfo-galactose

Type: D-saccharide, beta linking / Mass: 260.219 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₂O₉S / Feature type: SUBJECT OF INVESTIGATION

#3: Chemical

ChemComp-CA / CALCIUM ION

Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca

#4: Water

ChemComp-HOH / water /

Water

Mass: 18.015 Da / Num. of mol.: 186 / Source method: isolated from a natural source / Formula: H₂O

Has ligand of interest

Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 1.97 Å³/Da / Density % sol: 37.62 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 10 mg/ml of BT3109S1_15 with 10 mM 6S-Gal was crystallised in 30 % PEG 4000, 0.2 M ammonium acetate and sodium citrate pH 5.6.

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
Detector	Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Dec 14, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9762 Å / Relative weight: 1
Reflection	Resolution: 1.75→47.136 Å / Num. obs: 44392 / % possible obs: 99.5 % / Redundancy: 3.5 % / CC_1/2: 0.997 / Net I/σ(I): 8.8
Reflection shell	Resolution: 1.75→1.78 Å / Mean I/σ(I) obs: 1.2 / Num. unique obs: 2410 / CC_1/2: 0.493

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
xia2		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6S20

6s20

Resolution: 1.75→47.09 Å / Cor.coef. F_o:F_c: 0.967 / Cor.coef. F_o:F_c free: 0.948 / SU B: 3.793 / SU ML: 0.111 / Cross valid method: FREE R-VALUE / ESU R: 0.13 / ESU R Free: 0.12
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.217	2071	4.668 %
R_work	0.1836	42295	-
all	0.185	-	-
obs	-	44366	99.308 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 27.325 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.142 Å²	-0 Å²	0.242 Å²
2-	-	0.213 Å²	-0 Å²
3-	-	-	1.122 Å²

Refinement step

Cycle: LAST / Resolution: 1.75→47.09 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3731	0	17	186	3934

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.013	3999
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.017	3660
X-RAY DIFFRACTION	r_angle_refined_deg	1.492	1.65	5454
X-RAY DIFFRACTION	r_angle_other_deg	1.317	1.586	8461
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.113	5	518
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.428	22.843	204
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.505	15	644
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.537	15	22
X-RAY DIFFRACTION	r_chiral_restr	0.066	0.2	505
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	4703
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	925
X-RAY DIFFRACTION	r_nbd_refined	0.203	0.2	775
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.179	0.2	3474
X-RAY DIFFRACTION	r_nbtor_refined	0.162	0.2	1903
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.075	0.2	1764
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.17	0.2	205
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.567	0.2	1
X-RAY DIFFRACTION	r_metal_ion_refined	0.101	0.2	3
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.094	0.2	7
X-RAY DIFFRACTION	r_nbd_other	0.167	0.2	52
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.212	0.2	8
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.012	0.2	1
X-RAY DIFFRACTION	r_mcbond_it	1.854	2.772	2024
X-RAY DIFFRACTION	r_mcbond_other	1.853	2.772	2023
X-RAY DIFFRACTION	r_mcangle_it	2.496	4.155	2558
X-RAY DIFFRACTION	r_mcangle_other	2.496	4.155	2559
X-RAY DIFFRACTION	r_scbond_it	2.415	3.018	1975
X-RAY DIFFRACTION	r_scbond_other	2.417	3.019	1972
X-RAY DIFFRACTION	r_scangle_it	3.703	4.425	2896
X-RAY DIFFRACTION	r_scangle_other	3.704	4.426	2894
X-RAY DIFFRACTION	r_lrange_it	4.721	32.504	4439
X-RAY DIFFRACTION	r_lrange_other	4.711	32.445	4420

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.75-1.795	0.335	131	0.336	3126	X-RAY DIFFRACTION	98.8767
1.795-1.845	0.302	135	0.302	3031	X-RAY DIFFRACTION	99.3099
1.845-1.898	0.305	142	0.281	2964	X-RAY DIFFRACTION	99.392
1.898-1.956	0.279	163	0.248	2857	X-RAY DIFFRACTION	99.2768
1.956-2.021	0.272	128	0.235	2782	X-RAY DIFFRACTION	99.2835
2.021-2.091	0.24	104	0.213	2731	X-RAY DIFFRACTION	99.5785
2.091-2.17	0.248	132	0.203	2596	X-RAY DIFFRACTION	99.5257
2.17-2.259	0.22	155	0.178	2458	X-RAY DIFFRACTION	99.809
2.259-2.359	0.237	137	0.175	2417	X-RAY DIFFRACTION	99.7656
2.359-2.474	0.217	102	0.178	2308	X-RAY DIFFRACTION	99.6691
2.474-2.608	0.265	120	0.19	2202	X-RAY DIFFRACTION	99.871
2.608-2.766	0.215	124	0.177	2040	X-RAY DIFFRACTION	99.6317
2.766-2.957	0.228	124	0.174	1908	X-RAY DIFFRACTION	99.559
2.957-3.194	0.189	58	0.166	1850	X-RAY DIFFRACTION	99.4786
3.194-3.498	0.176	56	0.163	1706	X-RAY DIFFRACTION	98.9888
3.498-3.91	0.158	68	0.145	1493	X-RAY DIFFRACTION	98.548
3.91-4.514	0.136	72	0.136	1312	X-RAY DIFFRACTION	98.5755
4.514-5.525	0.206	57	0.144	1127	X-RAY DIFFRACTION	98.4206
5.525-7.799	0.219	35	0.169	890	X-RAY DIFFRACTION	99.1425
7.799-47.09	0.213	28	0.179	497	X-RAY DIFFRACTION	98.8701

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