PDB-8axt: Sialidases and Fucosidases of Akkermansia muciniphila are key for...

ID or keywords:

Entry

Database: PDB / ID: 8axt

Title

Sialidases and Fucosidases of Akkermansia muciniphila are key for rapid growth on colonic mucin and nutrient sharing amongst mucin-associated human gut microbiota

Components

Sialidase domain-containing protein

Keywords

HYDROLASE / Sialidase / Neuraminidase

Function / homology

Function and homology information

ganglioside catabolic process / oligosaccharide catabolic process / exo-alpha-sialidase / exo-alpha-sialidase activity / intracellular membrane-bounded organelle / metal ion binding / membrane / cytoplasm
Similarity search - Function

Biological species

Akkermansia muciniphila (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.59 Å

Authors

Sakanaka, H. / Nielsen, T.S. / Pichler, M.J. / Nordberg Karlsson, E. / Abou Hachem, M. / Morth, J.P.

Funding support

Denmark, Iraq, 2items

Citation

Journal: Nat Commun / Year: 2023
Title: Sialidases and fucosidases of Akkermansia muciniphila are crucial for growth on mucin and nutrient sharing with mucus-associated gut bacteria.
Authors: Shuoker, B. / Pichler, M.J. / Jin, C. / Sakanaka, H. / Wu, H. / Gascuena, A.M. / Liu, J. / Nielsen, T.S. / Holgersson, J. / Nordberg Karlsson, E. / Juge, N. / Meier, S. / Morth, J.P. / ...

History

Deposition	Aug 31, 2022	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Mar 1, 2023	Provider: repository / Type: Initial release
Revision 1.1	Apr 19, 2023	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Apr 3, 2024	Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.3	May 1, 2024	Group: Refinement description / Category: pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8axt.cif.gz	813.1 KB	Display	PDBx/mmCIF format
PDB format	pdb8axt.ent.gz	556.8 KB	Display	PDB format
PDBx/mmJSON format	8axt.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/ax/8axt ftp://data.pdbj.org/pub/pdb/validation_reports/ax/8axt	HTTPS FTP

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Related structure data

Related structure data	8axiC 8axsC 8ayrC 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	#113 - May 2009 Influenza Neuraminidase similarity (3) #231 - Mar 2019 Measles Virus Proteins similarity (1)

Deposited unit

A: Sialidase domain-containing protein

B: Sialidase domain-containing protein

hetero molecules

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

1

A: Sialidase domain-containing protein

hetero molecules

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

2

B: Sialidase domain-containing protein

hetero molecules

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

Unit cell

Length a, b, c (Å)	72.960, 56.790, 146.720
Angle α, β, γ (deg.)	90.000, 94.550, 90.000
Int Tables number	4
Space group name H-M	P12₁1
Space group name Hall	P2yb
Symmetry operation	#1: x,y,z #2: -x,y+1/2,-z

#1: Protein	Sialidase domain-containing protein Mass: 65149.410 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Akkermansia muciniphila (bacteria) / Gene: Amuc_1547 / Production host: Escherichia coli (E. coli) / References: UniProt: B2ULI1
#2: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1328 / 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: 2.33 Å³/Da / Density % sol: 47.11 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion / pH: 5.5 / Details: 25% PEG 3350, 0.1 M Bis tris, 0.2 MgCl2 / PH range: 5 -6

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9762 Å
Detector	Type: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Sep 25, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9762 Å / Relative weight: 1
Reflection	Resolution: 1.59→146.258 Å / Num. obs: 160846 / % possible obs: 99.8 % / Redundancy: 6.7 % / B_iso Wilson estimate: 15.12 Å² / CC_1/2: 0.99 / R_merge(I) obs: 0.3 / R_rim(I) all: 0.32 / Net I/σ(I): 6.7
Reflection shell	Resolution: 1.59→1.63 Å / Redundancy: 6.6 % / R_merge(I) obs: 1 / Num. unique obs: 11798 / CC_1/2: 0.32 / R split: 1 / R_pim(I) all: 1 / R_rim(I) all: 1 / R_sym value: 1 / % possible all: 99.8

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Processing

Software

Name	Version	Classification
PHENIX	1.19.2_4158	refinement
PHENIX	1.19.2_4158	refinement
xia2		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: alpha fold model

Resolution: 1.59→72.73 Å / SU ML: 0.1928 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.2374
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.202	8029	4.99 %
R_work	0.1683	152764	-
obs	0.17	160793	99.77 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 19.75 Å²

Refinement step

Cycle: LAST / Resolution: 1.59→72.73 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8994	0	7	1328	10329

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0095	9248
X-RAY DIFFRACTION	f_angle_d	1.0513	12540
X-RAY DIFFRACTION	f_chiral_restr	0.061	1322
X-RAY DIFFRACTION	f_plane_restr	0.0121	1648
X-RAY DIFFRACTION	f_dihedral_angle_d	6.8433	1247

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 (%)
1.59-1.61	0.3096	252	0.3008	4991	X-RAY DIFFRACTION	99.83
1.61-1.63	0.3378	274	0.2945	5137	X-RAY DIFFRACTION	99.71
1.63-1.65	0.3373	279	0.2872	4993	X-RAY DIFFRACTION	99.57
1.65-1.67	0.2981	283	0.276	5104	X-RAY DIFFRACTION	99.78
1.67-1.69	0.3014	270	0.2458	5009	X-RAY DIFFRACTION	99.87
1.69-1.71	0.2776	253	0.2376	5112	X-RAY DIFFRACTION	99.8
1.71-1.74	0.2901	234	0.2359	5108	X-RAY DIFFRACTION	99.83
1.74-1.76	0.283	266	0.2353	5015	X-RAY DIFFRACTION	99.91
1.76-1.79	0.2595	271	0.2265	5067	X-RAY DIFFRACTION	99.78
1.79-1.82	0.2634	263	0.2113	5109	X-RAY DIFFRACTION	99.74
1.82-1.85	0.2407	269	0.1992	5065	X-RAY DIFFRACTION	99.93
1.85-1.89	0.2127	265	0.192	5063	X-RAY DIFFRACTION	99.87
1.89-1.92	0.2149	293	0.1876	5058	X-RAY DIFFRACTION	99.76
1.92-1.96	0.2297	263	0.1777	5095	X-RAY DIFFRACTION	99.94
1.96-2	0.1974	261	0.1586	5044	X-RAY DIFFRACTION	99.72
2-2.05	0.2029	258	0.1572	5089	X-RAY DIFFRACTION	99.87
2.05-2.1	0.1964	291	0.1599	5118	X-RAY DIFFRACTION	99.96
2.1-2.16	0.1962	262	0.157	5065	X-RAY DIFFRACTION	99.78
2.16-2.22	0.2002	275	0.1564	5058	X-RAY DIFFRACTION	99.79
2.22-2.29	0.1999	266	0.1621	5094	X-RAY DIFFRACTION	99.76
2.29-2.38	0.1928	284	0.1445	5122	X-RAY DIFFRACTION	99.94
2.38-2.47	0.1651	222	0.1376	5120	X-RAY DIFFRACTION	99.96
2.47-2.58	0.183	295	0.1436	5105	X-RAY DIFFRACTION	99.91
2.58-2.72	0.185	258	0.1477	5117	X-RAY DIFFRACTION	99.87
2.72-2.89	0.1947	263	0.1517	5084	X-RAY DIFFRACTION	99.79
2.89-3.11	0.1822	278	0.16	5094	X-RAY DIFFRACTION	99.81
3.11-3.43	0.1782	285	0.1538	5157	X-RAY DIFFRACTION	99.63
3.43-3.92	0.1685	259	0.147	5105	X-RAY DIFFRACTION	99.41
3.92-4.94	0.1585	268	0.131	5178	X-RAY DIFFRACTION	99.56
4.94-72.73	0.196	269	0.1719	5288	X-RAY DIFFRACTION	99.06

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	2.39663248796	-0.277020410669	-0.577856659199	0.693945634076	-0.178831861314	1.13858019309	0.0486429354209	0.103106502638	0.120252416262	-0.0307193057695	0.0350905151354	0.0349524963476	-0.119501477128	-0.182033373841	-0.0904495479153	0.11960645951	0.0183124500066	-0.00453095586158	0.137070780001	0.0273182047152	0.13942578748	8.71282015757	16.0846143927	7.95921477592
2	2.3275132145	-0.605709533258	0.16227612173	3.61033998867	-0.186834591323	1.45143847401	-0.031464380343	-0.0693730538935	0.166545176688	0.0251609265628	0.0777673420061	0.154193715633	-0.205112227289	-0.238939048257	-0.0505363440665	0.105472276765	0.0246041879418	0.0124557485463	0.198056067064	0.0200833276315	0.144807296706	-3.39508385029	12.7956391785	19.9671806749
3	0.513036785453	-0.0291270207356	-0.00400856602118	0.301319370377	-0.0287489465134	0.480602912872	-0.00324963082996	-0.0223648745492	-0.00338535823535	-0.00982277986326	0.0128997647063	0.0375370285248	-0.0091448130669	-0.072675542269	-0.0192220741588	0.0919991711939	-0.006545833471	-0.00492812653858	0.0820539175934	-0.00417971676018	0.0997362109237	21.1740459461	0.0404831273147	19.0898378866
4	0.433679748902	-0.0957843325838	-0.204573664095	0.512773973959	0.208687671938	1.03739862258	-0.0306165434464	-0.0962425373814	-0.0598196853047	0.0487043252466	0.0478524285444	-0.0606839180312	0.110691608676	0.121584164424	-0.0313651075776	0.0874194398602	0.0121715365549	-0.00319766830811	0.0914359343033	0.00862443011696	0.113155839766	40.5447688245	-13.3482334474	21.9705627166
5	2.25848695389	0.253290708277	0.517100613365	0.7434508908	-0.315665433277	1.0415572382	0.039249582258	-0.13376595656	-0.144273465759	0.0340790961466	0.0977059996311	0.0926811802752	0.176911118694	-0.305332737449	-0.0168615480737	0.15682801767	-0.056236228149	-0.0187904456795	0.194573151699	0.0535373072962	0.168161892005	4.58647095157	10.9768072544	61.0616022942
6	0.903151642519	0.570989001945	-0.131198844321	1.63144053562	-0.360578232698	0.644375942646	0.040746321079	0.0785870572761	-0.329894336306	-0.179773441604	0.163053169837	0.181730867998	0.309297545692	-0.435219442866	0.154903898079	0.180809183552	-0.0946293157841	-0.0635114248152	0.33670486414	0.0798983493368	0.27139569776	-5.75491780565	14.4328622082	47.469538823
7	1.99380419725	0.280330845957	-0.368792146148	0.511463430182	-0.251098788353	0.780016437153	0.0172119178009	0.0990224524988	0.0708258130484	-0.0249144191028	0.0869231964106	0.126218002171	-0.0137916442306	-0.245533484417	-0.0334441597743	0.108214362348	0.00348330932827	-0.0027578220279	0.174358141614	0.04478138264	0.144784626961	5.88011046449	30.1823544885	43.4670275302
8	1.09587456924	-0.182758521587	-0.106132405687	0.57691237356	-0.0613811175915	0.867425685348	0.0241702428121	0.0335339280193	0.00360237903817	-0.0347178181657	0.0489902889265	0.0661361037171	-0.0365269370543	-0.115130870892	-0.0658720742766	0.0805753867106	0.00324329043865	0.0178590683543	0.0731693164468	0.0109769788594	0.0958648385216	16.7611841307	29.9280868217	51.1811226278
9	0.751871978058	0.119286725236	-0.361572473332	0.60709012699	-0.0651308577859	0.778522010425	0.0165063267888	-0.0195584598972	-0.0544265518461	0.0623760068091	0.0128718468371	0.0177579924861	0.0382681579106	-0.00810684152936	-0.0220194964533	0.120950266591	0.0158896073172	-0.00440289587697	0.0805737928516	0.00898778494057	0.0960618453736	28.4524994307	23.0808802126	58.0678435781
10	0.717405767212	0.184205556912	0.165956725035	0.80151929916	0.235112461227	1.37380270956	0.00167558068903	0.0635320151075	0.0200630294892	-0.0119055906779	0.0525974298117	-0.101607301666	-0.0654509380601	0.279928236944	-0.0813095707467	0.0952729592046	-0.0143540027307	0.00116304562781	0.10853325102	0.0127367789427	0.0890805367403	40.1304691599	34.3439978022	49.6559408182
11	1.44222349304	-0.150224195877	0.335977141957	1.06688321504	0.0180804227985	1.04893009963	-0.0338767717809	0.104646010349	0.113785002931	0.0495672263711	0.00779084691215	-0.0649673994988	-0.190627577164	0.146093759402	-0.00444780741515	0.148897553506	-0.0316415965619	0.00623086351787	0.0982824096457	0.0116803555263	0.10351193048	37.2025500432	43.9288751466	53.2538804009

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid 25 through 127 )	A	A	25 - 127	1 - 103
2	2	chain 'A' and (resid 128 through 182 )	A	A	128 - 182	104 - 158
3	3	chain 'A' and (resid 183 through 436 )	A	A	183 - 436	159 - 412
4	4	chain 'A' and (resid 437 through 595 )	A	A	437 - 595	413 - 571
5	5	chain 'B' and (resid 25 through 127 )	B	B	25 - 127	1 - 103
6	6	chain 'B' and (resid 128 through 182 )	B	B	128 - 182	104 - 158
7	7	chain 'B' and (resid 183 through 250 )	B	B	183 - 250	159 - 226
8	8	chain 'B' and (resid 251 through 333 )	B	B	251 - 333	227 - 309
9	9	chain 'B' and (resid 334 through 436 )	B	B	334 - 436	310 - 412
10	10	chain 'B' and (resid 437 through 492 )	B	B	437 - 492	413 - 468
11	11	chain 'B' and (resid 493 through 595 )	B	B	493 - 595	469 - 571

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