PDB-9eob: Engineered GH181 sialidase from Akkermansia muciniphila

ID or keywords:

Entry

Database: PDB / ID: 9eob

Title

Engineered GH181 sialidase from Akkermansia muciniphila

Components

exo-alpha-sialidase

Keywords

HYDROLASE / Akkermansia muciniphila / gut microbiome / mucin / retaining mechanism / Sialidase

Function / homology

BNR repeat-like domain / Sialidase / Sialidase superfamily / NICKEL (II) ION / DI(HYDROXYETHYL)ETHER / Exo-alpha-sialidase

Function and homology information

Biological species

Akkermansia muciniphila ATCC BAA-835 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.77 Å

Authors

Pichler, M.J. / Banerjee, S. / Nielsen, T.S. / Morth, J.P. / Abou Hachem, M.

Funding support

Denmark, 1items

Citation

Journal: Acs Catalysis / Year: 2025
Title: Engineered GH181 sialidase from Akkermansia muciniphila
Authors: Pichler, M.J. / Corbella, M. / Banerjee, S. / Nielsen, T.S. / Morth, J.P. / Rovira, C. / Abou Hachem, M.

History

Deposition	Mar 14, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Mar 26, 2025	Provider: repository / Type: Initial release
Revision 1.1	May 21, 2025	Group: Database references / Category: citation Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.year

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9eob.cif.gz	154 KB	Display	PDBx/mmCIF format
PDB format	pdb9eob.ent.gz	111.3 KB	Display	PDB format
PDBx/mmJSON format	9eob.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/eo/9eob ftp://data.pdbj.org/pub/pdb/validation_reports/eo/9eob	HTTPS FTP

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Related structure data

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	#113 - May 2009 Influenza Neuraminidase similarity (1) #231 - Mar 2019 Measles Virus Proteins similarity (1)

Deposited unit

A: exo-alpha-sialidase

hetero molecules

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

1

Idetical with deposited unit
defined by author
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	74.670, 88.189, 99.585
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

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Protein , 1 types, 1 molecules A

#1: Protein	exo-alpha-sialidase Mass: 64915.113 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Akkermansia muciniphila ATCC BAA-835 (bacteria) Gene: HXS70_08015 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7G6DVF6, exo-alpha-sialidase

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Non-polymers , 5 types, 594 molecules

#2: Chemical	ChemComp-NI / NICKEL (II) ION Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#5: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 566 / Source method: isolated from a natural source / Formula: H₂O

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Details

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: 2.53 Å³/Da / Density % sol: 51.3 %
Crystal grow	Temperature: 291.15 K / Method: vapor diffusion, sitting drop Details: 10% PEG 8000 W/V, 9% Ethylene glycol (v/v), 0.1M HEPES pH 7.5

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.98 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 3, 2024
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.98 Å / Relative weight: 1
Reflection	Resolution: 1.77→66.02 Å / Num. obs: 64414 / % possible obs: 99 % / Redundancy: 9.6 % / CC_1/2: 0.998 / Net I/σ(I): 11.7
Reflection shell	Resolution: 1.77→1.8 Å / Num. unique obs: 6073 / CC_1/2: 0.503

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0419	refinement
autoPROC		data reduction
TRUNCATE		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.77→66.02 Å / Cor.coef. F_o:F_c: 0.972 / Cor.coef. F_o:F_c free: 0.954 / SU B: 2.43 / SU ML: 0.073 / Cross valid method: FREE R-VALUE / ESU R: 0.102 / ESU R Free: 0.104
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1953	3267	5.072 %
R_work	0.1552	61147	-
all	0.157	-	-
obs	-	64414	99.473 %

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: 24.106 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.045 Å²	-0 Å²	-0 Å²
2-	-	0.647 Å²	-0 Å²
3-	-	-	-0.692 Å²

Refinement step

Cycle: LAST / Resolution: 1.77→66.02 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4572	0	88	566	5226

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.012	4852
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.016	4563
X-RAY DIFFRACTION	r_angle_refined_deg	1.519	1.674	6556
X-RAY DIFFRACTION	r_angle_other_deg	0.515	1.593	10511
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.662	5	600
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	6.963	5	41
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.187	10	798
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	17.127	10	226
X-RAY DIFFRACTION	r_chiral_restr	0.074	0.2	684
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	5867
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1157
X-RAY DIFFRACTION	r_nbd_refined	0.2	0.2	782
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.194	0.2	4288
X-RAY DIFFRACTION	r_nbtor_refined	0.173	0.2	2259
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.087	0.2	2547
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.167	0.2	420
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.149	0.2	5
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.228	0.2	22
X-RAY DIFFRACTION	r_nbd_other	0.182	0.2	63
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.143	0.2	35
X-RAY DIFFRACTION	r_mcbond_it	2.166	2.372	2370
X-RAY DIFFRACTION	r_mcbond_other	2.165	2.372	2370
X-RAY DIFFRACTION	r_mcangle_it	2.992	4.255	2980
X-RAY DIFFRACTION	r_mcangle_other	2.992	4.255	2981
X-RAY DIFFRACTION	r_scbond_it	3.386	2.739	2482
X-RAY DIFFRACTION	r_scbond_other	3.385	2.74	2483
X-RAY DIFFRACTION	r_scangle_it	5.063	4.796	3576
X-RAY DIFFRACTION	r_scangle_other	5.062	4.798	3577
X-RAY DIFFRACTION	r_lrange_it	6.56	27.722	5328
X-RAY DIFFRACTION	r_lrange_other	6.417	26.224	5203

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 (%)
1.77-1.816	0.287	242	0.264	4207	X-RAY DIFFRACTION	94.2186
1.816-1.866	0.256	202	0.236	4328	X-RAY DIFFRACTION	98.6283
1.866-1.92	0.23	244	0.205	4253	X-RAY DIFFRACTION	99.9778
1.92-1.979	0.218	226	0.184	4100	X-RAY DIFFRACTION	100
1.979-2.044	0.224	222	0.17	4024	X-RAY DIFFRACTION	100
2.044-2.115	0.222	193	0.175	3912	X-RAY DIFFRACTION	100
2.115-2.195	0.174	202	0.141	3735	X-RAY DIFFRACTION	100
2.195-2.285	0.18	197	0.144	3618	X-RAY DIFFRACTION	100
2.285-2.386	0.198	189	0.145	3482	X-RAY DIFFRACTION	100
2.386-2.502	0.19	200	0.147	3321	X-RAY DIFFRACTION	100
2.502-2.637	0.179	173	0.143	3140	X-RAY DIFFRACTION	100
2.637-2.797	0.191	157	0.144	3005	X-RAY DIFFRACTION	100
2.797-2.99	0.181	143	0.138	2859	X-RAY DIFFRACTION	100
2.99-3.229	0.184	142	0.148	2641	X-RAY DIFFRACTION	100
3.229-3.536	0.219	118	0.163	2467	X-RAY DIFFRACTION	100
3.536-3.952	0.191	128	0.156	2209	X-RAY DIFFRACTION	100
3.952-4.561	0.148	98	0.128	1977	X-RAY DIFFRACTION	100
4.561-5.579	0.166	82	0.119	1709	X-RAY DIFFRACTION	100
5.579-7.862	0.207	57	0.163	1349	X-RAY DIFFRACTION	100
7.862-66.02	0.214	51	0.169	793	X-RAY DIFFRACTION	99.8817

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