PDB-9sf6: Amuc0953 N-terminal domain

ID or keywords:

Entry

Database: PDB / ID: 9sf6

Title

Amuc0953 N-terminal domain

Components

Sulfatase

Keywords

SUGAR BINDING PROTEIN / Carbohydrate binding module / 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 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 19, 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	9sf6.cif.gz	195.4 KB	Display	PDBx/mmCIF format
PDB format	pdb9sf6.ent.gz	148.5 KB	Display	PDB format
PDBx/mmJSON format	9sf6.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/sf/9sf6 ftp://data.pdbj.org/pub/pdb/validation_reports/sf/9sf6	HTTPS FTP

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Related structure data

Related structure data	9s7xC 9s85C 9s88C 9s8aC 9s8fC 9s8xC 9s8yC 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

B: Sulfatase

A: Sulfatase

hetero molecules

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

1

B: Sulfatase

hetero molecules

defined by author
Evidence: gel filtration
49.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

A: Sulfatase

hetero molecules

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

Unit cell

Length a, b, c (Å)	100.44, 59.15, 111.12
Angle α, β, γ (deg.)	90, 95.11, 90
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Sulfatase Mass: 48901.648 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: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 265 / 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: 3.36 Å³/Da / Density % sol: 63.41 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / Details: 20 % PEG 3350, 0.2 M NaI 25 mg/ml protein

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

Diamond

/ Beamline: I04 / Wavelength: 0.8 Å

Detector

Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 14, 2022

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.8 Å / Relative weight: 1

Reflection

Resolution: 2→55.34 Å / Num. obs: 88190 / % possible obs: 99.9 % / Redundancy: 6.9 % / CC_1/2: 0.994 / R_merge(I) obs: 0.193 / R_pim(I) all: 0.121 / R_rim(I) all: 0.229 / Χ²: 1.03 / Net I/σ(I): 6.6

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
10.77-55.34	5.7	0.061	18.8	612	0.992	0.039	0.073	0.87	98
2-2.04	7	2.063	1.2	4512	0.364	1.28	2.433	0.97	99.9

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2→55.34 Å / Cor.coef. F_o:F_c: 0.965 / Cor.coef. F_o:F_c free: 0.948 / SU B: 5.507 / SU ML: 0.135 / Cross valid method: FREE R-VALUE / ESU R: 0.142 / ESU R Free: 0.139
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2321	4426	5.02 %
R_work	0.1921	83749	-
all	0.194	-	-
obs	-	88175	99.904 %

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: 44.953 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	3.878 Å²	-0 Å²	0.645 Å²
2-	-	-2.079 Å²	-0 Å²
3-	-	-	-1.885 Å²

Refinement step

Cycle: LAST / Resolution: 2→55.34 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6878	0	77	265	7220

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.012	7060
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	6442
X-RAY DIFFRACTION	r_angle_refined_deg	1.555	1.782	9621
X-RAY DIFFRACTION	r_angle_other_deg	0.539	1.733	14804
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.572	5	934
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	8.333	5	44
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.427	10	1054
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	14.793	10	301
X-RAY DIFFRACTION	r_chiral_restr	0.071	0.2	1095
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	8612
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1580
X-RAY DIFFRACTION	r_nbd_refined	0.199	0.2	1112
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.197	0.2	5883
X-RAY DIFFRACTION	r_nbtor_refined	0.172	0.2	3419
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.087	0.2	3875
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.138	0.2	318
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.21	0.2	24
X-RAY DIFFRACTION	r_nbd_other	0.223	0.2	68
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.167	0.2	8
X-RAY DIFFRACTION	r_mcbond_it	3.558	4.259	3742
X-RAY DIFFRACTION	r_mcbond_other	3.558	4.258	3742
X-RAY DIFFRACTION	r_mcangle_it	5.095	7.638	4674
X-RAY DIFFRACTION	r_mcangle_other	5.097	7.639	4675
X-RAY DIFFRACTION	r_scbond_it	4.999	4.852	3318
X-RAY DIFFRACTION	r_scbond_other	4.904	4.79	3259
X-RAY DIFFRACTION	r_scangle_it	7.706	8.65	4947
X-RAY DIFFRACTION	r_scangle_other	7.633	8.545	4858
X-RAY DIFFRACTION	r_lrange_it	9.342	43.16	7299
X-RAY DIFFRACTION	r_lrange_other	9.333	43.187	7262

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
2-2.052	0.359	338	0.336	6141	0.337	6484	0.874	0.89	99.9229	0.336
2.052-2.108	0.337	297	0.321	6025	0.322	6323	0.893	0.907	99.9842	0.318
2.108-2.169	0.312	265	0.298	5843	0.299	6111	0.919	0.921	99.9509	0.293
2.169-2.236	0.3	334	0.283	5641	0.284	5984	0.922	0.933	99.8496	0.276
2.236-2.309	0.291	307	0.262	5442	0.264	5753	0.927	0.945	99.9305	0.252
2.309-2.39	0.294	280	0.245	5331	0.248	5615	0.938	0.955	99.9288	0.234
2.39-2.48	0.259	285	0.222	5130	0.224	5416	0.953	0.965	99.9815	0.211
2.48-2.581	0.277	274	0.218	4982	0.221	5257	0.955	0.97	99.981	0.205
2.581-2.695	0.268	264	0.206	4703	0.21	4968	0.956	0.975	99.9799	0.194
2.695-2.827	0.25	224	0.2	4539	0.202	4763	0.958	0.977	100	0.189
2.827-2.979	0.24	208	0.199	4357	0.201	4566	0.963	0.976	99.9781	0.192
2.979-3.159	0.232	198	0.192	4112	0.193	4312	0.962	0.977	99.9536	0.186
3.159-3.377	0.217	217	0.172	3843	0.174	4062	0.965	0.981	99.9508	0.173
3.377-3.646	0.194	208	0.155	3559	0.157	3770	0.978	0.986	99.9204	0.159
3.646-3.992	0.178	169	0.145	3338	0.147	3510	0.981	0.988	99.9145	0.157
3.992-4.461	0.18	160	0.136	3008	0.138	3175	0.985	0.99	99.7795	0.152
4.461-5.145	0.157	122	0.123	2665	0.125	2793	0.985	0.992	99.7852	0.146
5.145-6.288	0.176	124	0.159	2281	0.159	2408	0.983	0.987	99.8754	0.183
6.288-8.836	0.265	100	0.178	1772	0.182	1878	0.964	0.981	99.6805	0.206
8.836-55.34	0.273	52	0.241	1037	0.243	1108	0.965	0.972	98.2852	0.293

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