PDB-9s8a: Amuc0451_S1_20

ID or keywords:

Entry

Database: PDB / ID: 9s8a

Title

Amuc0451_S1_20

Components

Sulfatase

Keywords

HYDROLASE / Carbohydrate sulfatase / mucin / Akkermansia muciniphila / Sulfation

Function / homology

Function and homology information

: / PA14/GLEYA domain / PA14 domain profile. / PA14 domain / Sulfatase, N-terminal / Sulfatase / PA14 / PA14 domain / Alkaline-phosphatase-like, core domain superfamily
Similarity search - Domain/homology

Biological species

Akkermansia muciniphila ATCC BAA-835 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.6 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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Download

PDBx/mmCIF format	9s8a.cif.gz	720.3 KB	Display	PDBx/mmCIF format
PDB format	pdb9s8a.ent.gz	472.3 KB	Display	PDB format
PDBx/mmJSON format	9s8a.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/s8/9s8a ftp://data.pdbj.org/pub/pdb/validation_reports/s8/9s8a	HTTPS FTP

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Related structure data

Related structure data	9s7xC 9s85C 9s88C 9s8fC 9s8xC 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) #50 - Feb 2004 Glycolytic Enzymes similarity (1)

Deposited unit

A: Sulfatase

B: Sulfatase

hetero molecules

152 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
76.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Sulfatase

hetero molecules

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

Unit cell

Length a, b, c (Å)	113.66, 59.9, 123.72
Angle α, β, γ (deg.)	90, 115.75, 90
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Sulfatase Mass: 75251.828 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Akkermansia muciniphila ATCC BAA-835 (bacteria) Gene: CXT95_07920 / Production host: Escherichia coli (E. coli) / References: UniProt: A0AAX0WNV9
#2: Chemical	... ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO₄
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 948 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
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: 2.52 Å³/Da / Density % sol: 51.24 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 20 % w/v PEG 3350, 0.1 M Bis-Tris propane 7.5, 0.02 M Sodium/potassium phosphate 40 mg/ml Amuc0451

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / 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: 1.6→59.9 Å / Num. obs: 1291159 / % possible obs: 100 % / Redundancy: 6.5 % / CC_1/2: 0.998 / Net I/σ(I): 10.3
Reflection shell	Resolution: 1.6→1.63 Å / Mean I/σ(I) obs: 1.4 / Num. unique obs: 55288 / CC_1/2: 0.549

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.6→51.754 Å / Cor.coef. F_o:F_c: 0.974 / Cor.coef. F_o:F_c free: 0.965 / SU B: 5.842 / SU ML: 0.083 / Cross valid method: FREE R-VALUE / ESU R: 0.097 / ESU R Free: 0.078
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1915	9908	5.01 %
R_work	0.1556	187874	-
all	0.157	-	-
obs	-	197782	99.961 %

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: 23.68 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.642 Å²	-0 Å²	0.096 Å²
2-	-	-4.146 Å²	-0 Å²
3-	-	-	0.964 Å²

Refinement step

Cycle: LAST / Resolution: 1.6→51.754 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10611	0	120	948	11679

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.012	11260
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	10493
X-RAY DIFFRACTION	r_angle_refined_deg	1.681	1.816	15254
X-RAY DIFFRACTION	r_angle_other_deg	0.6	1.776	24234
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.893	5	1422
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	7.658	5	78
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.106	10	1814
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.656	10	514
X-RAY DIFFRACTION	r_chiral_restr	0.091	0.2	1567
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	13636
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	2648
X-RAY DIFFRACTION	r_nbd_refined	0.212	0.2	2071
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.195	0.2	9522
X-RAY DIFFRACTION	r_nbtor_refined	0.176	0.2	5438
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.082	0.2	5727
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.134	0.2	777
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.006	0.2	1
X-RAY DIFFRACTION	r_metal_ion_refined	0.28	0.2	12
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.201	0.2	3
X-RAY DIFFRACTION	r_nbd_other	0.157	0.2	25
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.203	0.2	19
X-RAY DIFFRACTION	r_mcbond_it	4.971	2.179	5604
X-RAY DIFFRACTION	r_mcbond_other	4.971	2.179	5605
X-RAY DIFFRACTION	r_mcangle_it	6.978	3.936	7054
X-RAY DIFFRACTION	r_mcangle_other	6.979	3.937	7055
X-RAY DIFFRACTION	r_scbond_it	6.002	2.396	5656
X-RAY DIFFRACTION	r_scbond_other	5.986	2.396	5649
X-RAY DIFFRACTION	r_scangle_it	8.552	4.272	8200
X-RAY DIFFRACTION	r_scangle_other	8.539	4.271	8189
X-RAY DIFFRACTION	r_lrange_it	13.078	21.743	12578
X-RAY DIFFRACTION	r_lrange_other	12.349	21.086	12385
X-RAY DIFFRACTION	r_rigid_bond_restr	7.257	3	21753

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
1.6-1.642	0.329	713	0.275	13812	0.277	14526	0.939	0.974	99.9931	0.263
1.642-1.686	0.282	718	0.255	13483	0.257	14201	0.963	0.978	100	0.24
1.686-1.735	0.258	700	0.23	13072	0.232	13774	0.964	0.982	99.9855	0.21
1.735-1.789	0.282	667	0.211	12713	0.215	13380	0.958	0.984	100	0.188
1.789-1.847	0.242	670	0.192	12330	0.195	13000	0.97	0.986	100	0.165
1.847-1.912	0.217	649	0.17	11942	0.173	12595	0.973	0.989	99.9682	0.144
1.912-1.984	0.215	595	0.166	11511	0.169	12107	0.974	0.988	99.9917	0.143
1.984-2.065	0.204	554	0.154	11188	0.156	11745	0.977	0.99	99.9745	0.134
2.065-2.157	0.187	545	0.142	10630	0.144	11176	0.98	0.991	99.9911	0.127
2.157-2.262	0.201	547	0.146	10200	0.148	10752	0.976	0.99	99.9535	0.132
2.262-2.384	0.184	494	0.132	9712	0.134	10208	0.981	0.992	99.9804	0.122
2.384-2.528	0.183	522	0.131	9150	0.134	9673	0.981	0.991	99.9897	0.122
2.528-2.702	0.179	448	0.134	8649	0.137	9099	0.982	0.99	99.978	0.13
2.702-2.918	0.167	451	0.13	8021	0.132	8477	0.983	0.991	99.941	0.131
2.918-3.195	0.177	387	0.141	7411	0.142	7811	0.98	0.989	99.8336	0.146
3.195-3.571	0.189	354	0.155	6737	0.157	7100	0.978	0.987	99.8732	0.167
3.571-4.12	0.151	291	0.136	5991	0.137	6288	0.987	0.99	99.9046	0.155
4.12-5.038	0.144	269	0.13	5051	0.13	5327	0.989	0.992	99.8686	0.157
5.038-7.091	0.21	214	0.174	3972	0.176	4190	0.981	0.988	99.9045	0.206
7.091-51.754	0.15	120	0.18	2298	0.179	2423	0.988	0.981	99.7936	0.22

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