PDB-9s8x: Amuc0953_S1_20 in complex with D-Galactose

ID or keywords:

Entry

Database: PDB / ID: 9s8x

Title

Amuc0953_S1_20 in complex with D-Galactose

Components

Sulfatase

Keywords

HYDROLASE / Carbohydrate sulfatase / mucin / Akkermansia muciniphila / Sulfation

Function / homology

Function and homology information

: / Putative binding domain, N-terminal / Bacteroidetes-Associated Carbohydrate-binding Often N-terminal / PA14/GLEYA domain / PA14 domain profile. / PA14 domain / Sulfatase, N-terminal / Sulfatase / PA14 / PA14 domain ...
Similarity search - Domain/homology

Biological species

Akkermansia muciniphila ATCC BAA-835 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.9 Å

Authors

Dey, D. / Cartmell, A.

Funding support

United Kingdom, 1items

Citation

Journal: To Be Published
Title: The role of Akkermansia muciniphila sulfatases in colonic mucin utilisation
Authors: Dey, D. / Salman, N.D. / Tomlinson, C.W.E. / Gugel, S. / Chunsheng, J. / Raba, G. / Nilsson, M. / McIver, Z. / Simpkin, A. / Davy, M. / Rigden, D.J. / Czjzek, M. / Byrne, D.P. / Case, A. / ...

History

Deposition	Aug 5, 2025	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jun 3, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	9s8x.cif.gz	1.1 MB	Display	PDBx/mmCIF format
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PDBx/mmJSON format	9s8x.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/s8/9s8x ftp://data.pdbj.org/pub/pdb/validation_reports/s8/9s8x	HTTPS FTP

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Related structure data

Related structure data	9s7xC 9s85C 9s88C 9s8aC 9s8fC 9s8yC 9sf6C C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#28 - Apr 2002 Anthrax Toxin similarity (5) #156 - Dec 2012 ABO Blood Type Glycosyltransferases similarity (1) #198 - Jun 2016 Beta-galactosidase similarity (1) #50 - Feb 2004 Glycolytic Enzymes similarity (1)

Deposited unit

A: Sulfatase

B: Sulfatase

hetero molecules

272 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Sulfatase

hetero molecules

defined by author
Evidence: light scattering
136 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Sulfatase

hetero molecules

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

Unit cell

Length a, b, c (Å)	187.28, 187.28, 221.77
Angle α, β, γ (deg.)	90, 90, 90
Int Tables number	80
Space group name H-M	I4₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details (eV)
1	1	A
2	1	B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: PRO / End label comp-ID: PRO / Auth seq-ID: 23 - 1285 / Label seq-ID: 1 - 1263

Dom-ID	Auth asym-ID	Label asym-ID
1	A	A
2	B	B

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

#1: Protein

Sulfatase

Mass: 135282.609 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Akkermansia muciniphila ATCC BAA-835 (bacteria)
Gene: Amuc_0953 / Production host:

Escherichia coli (E. coli) / References: UniProt: B2UQQ0

#2: Sugar

ChemComp-GAL / beta-D-galactopyranose / beta-D-galactose / D-galactose / galactose

Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₁₂O₆ / Feature type: SUBJECT OF INVESTIGATION

#3: Chemical

ChemComp-IOD / IODIDE ION

Mass: 126.904 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: I

#4: Chemical

ChemComp-CA / CALCIUM ION

Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca

Has ligand of interest

Y

Has protein modification

N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.59 Å³/Da / Density % sol: 65.77 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 20 % PEG 3350 0.2 M Sodium Iodide 55 mg/ml Amuc0953 with 100 mM D-Galactose

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1 Å
Detector	Type: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Jan 31, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.9→78.476 Å / Num. obs: 1156298 / % possible obs: 100 % / Redundancy: 6.5 % / CC_1/2: 0.998 / Net I/σ(I): 9.9
Reflection shell	Resolution: 2.9→2.95 Å / Num. unique obs: 61502 / CC_1/2: 0.641

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0430 (refmacat 0.4.105)	refinement
xia2		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.9→78.476 Å / Cor.coef. F_o:F_c: 0.948 / Cor.coef. F_o:F_c free: 0.942 / SU B: 47.825 / SU ML: 0.362 / Cross valid method: FREE R-VALUE / ESU R: 1.435 / ESU R Free: 0.37
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2566	4384	5.201 %
R_work	0.2118	79915	-
all	0.214	-	-
obs	-	84299	99.956 %

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: 90.956 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.084 Å²	0 Å²	0 Å²
2-	-	-2.084 Å²	0 Å²
3-	-	-	4.169 Å²

Refinement step

Cycle: LAST / Resolution: 2.9→78.476 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	19044	0	30	0	19074

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.012	19510
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	17732
X-RAY DIFFRACTION	r_angle_refined_deg	1.558	1.794	26564
X-RAY DIFFRACTION	r_angle_other_deg	0.538	1.743	40818
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.726	5	2524
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	10.994	5	132
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.136	10	2928
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	14.467	10	884
X-RAY DIFFRACTION	r_chiral_restr	0.07	0.2	2886
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	23918
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	4558
X-RAY DIFFRACTION	r_nbd_refined	0.234	0.2	3740
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.211	0.2	17058
X-RAY DIFFRACTION	r_nbtor_refined	0.182	0.2	9510
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.085	0.2	10692
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.147	0.2	501
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.01	0.2	2
X-RAY DIFFRACTION	r_metal_ion_refined	0.502	0.2	10
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.18	0.2	20
X-RAY DIFFRACTION	r_nbd_other	0.176	0.2	135
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.268	0.2	7
X-RAY DIFFRACTION	r_mcbond_it	5.666	6.365	10102
X-RAY DIFFRACTION	r_mcbond_other	5.666	6.365	10102
X-RAY DIFFRACTION	r_mcangle_it	8.407	11.446	12624
X-RAY DIFFRACTION	r_mcangle_other	8.407	11.446	12625
X-RAY DIFFRACTION	r_scbond_it	6.776	6.786	9408
X-RAY DIFFRACTION	r_scbond_other	6.776	6.786	9409
X-RAY DIFFRACTION	r_scangle_it	10.223	12.252	13940
X-RAY DIFFRACTION	r_scangle_other	10.222	12.252	13941
X-RAY DIFFRACTION	r_lrange_it	13.935	77.765	81821
X-RAY DIFFRACTION	r_lrange_other	13.935	77.765	81822
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.072	0.05	40059

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.07194	0.05012
1	2	B	X-RAY DIFFRACTION	Local ncs	0.07194	0.05012

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
2.9-2.975	0.459	326	0.439	5927	0.44	6253	0.837	0.853	100	0.431
2.975-3.057	0.4	350	0.402	5673	0.402	6023	0.871	0.882	100	0.389
3.057-3.145	0.406	286	0.366	5612	0.368	5900	0.879	0.908	99.9661	0.347
3.145-3.242	0.366	322	0.334	5394	0.335	5721	0.911	0.929	99.9126	0.307
3.242-3.348	0.365	295	0.304	5259	0.307	5555	0.915	0.944	99.982	0.271
3.348-3.465	0.297	317	0.271	5064	0.272	5386	0.942	0.958	99.9072	0.238
3.465-3.596	0.271	287	0.246	4894	0.247	5181	0.959	0.965	100	0.214
3.596-3.742	0.304	230	0.24	4740	0.242	4972	0.948	0.968	99.9598	0.206
3.742-3.908	0.256	264	0.201	4535	0.204	4800	0.96	0.978	99.9792	0.172
3.908-4.098	0.221	249	0.17	4307	0.172	4556	0.972	0.984	100	0.149
4.098-4.32	0.215	209	0.149	4159	0.152	4369	0.974	0.988	99.9771	0.135
4.32-4.581	0.199	213	0.138	3881	0.141	4095	0.978	0.989	99.9756	0.132
4.581-4.896	0.169	186	0.135	3676	0.137	3863	0.983	0.99	99.9741	0.132
4.896-5.286	0.21	195	0.153	3425	0.156	3624	0.974	0.988	99.8896	0.153
5.286-5.788	0.212	161	0.162	3162	0.165	3323	0.976	0.987	100	0.164
5.788-6.467	0.218	134	0.168	2889	0.17	3023	0.973	0.985	100	0.173
6.467-7.459	0.196	124	0.145	2543	0.147	2667	0.978	0.989	100	0.155
7.459-9.115	0.216	97	0.159	2163	0.162	2260	0.969	0.987	100	0.179
9.115-12.804	0.206	86	0.178	1659	0.179	1746	0.98	0.987	99.9427	0.197
12.804-78.476	0.281	53	0.293	953	0.292	1015	0.963	0.941	99.1133	0.337

Refinement TLS params.

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

ID	L11 (°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)
1	1.2753	0.2178	-0.3717	0.4747	-0.0892	0.2462	0.1221	0.0042	0.2182	0.1382	-0.0383	0.1985	-0.1248	-0.005	-0.0838	0.142	-0.0141	0.0469	0.0119	-0.0458	0.2997	62.6955	-3.6439	55.4071
2	0.5196	-0.2617	0.0695	1.3331	-0.3317	0.2235	-0.0472	-0.1552	-0.2076	0.0361	0.1335	0.2198	0.0059	-0.1187	-0.0863	0.0103	0.0123	0.0306	0.1357	0.0499	0.2709	3.6214	-30.9524	4.5517

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	A	23 - 1285
2	X-RAY DIFFRACTION	2	ALL	B	23 - 1285

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