PDB-8hls: Crystal structure of the sialidase Am1547 from A.muciniphila

ID or keywords:

Entry

Database: PDB / ID: 8hls

Title

Crystal structure of the sialidase Am1547 from A.muciniphila

Components

Sialidase domain-containing protein

Keywords

HYDROLASE /

sialidase

Function / homology

BNR repeat-like domain /

Sialidase / Sialidase superfamily /

metal ion binding / Sialidase domain-containing protein

Function and homology information

Biological species

Akkermansia muciniphila ATCC BAA-835 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.04 Å

Authors

Rui, B. / Xinyue, T.

Funding support

China, 1items

Citation

Journal: To Be Published
Title: Structural analysis of a novel sialidase from Akkermansia muciniphila reveals a distinct catalytic motif in GH33 family
Authors: Xinyue, T. / Rui, B.

History

Deposition	Nov 30, 2022	Deposition site: PDBJ / Processing site: RCSB
Revision 1.0	Jun 5, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8hls.cif.gz	511.9 KB	Display	PDBx/mmCIF format
PDB format	pdb8hls.ent.gz	372.9 KB	Display	PDB format
PDBx/mmJSON format	8hls.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/hl/8hls ftp://data.pdbj.org/pub/pdb/validation_reports/hl/8hls	HTTPS FTP

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Related structure data

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 (1) #231 - Mar 2019 Measles Virus Proteins similarity (1)

Deposited unit

A: Sialidase domain-containing protein

B: Sialidase domain-containing protein

hetero molecules

135 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
67.4 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
67.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	72.160, 56.771, 145.932
Angle α, β, γ (deg.)	90.000, 94.010, 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

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
d_1	ens_1	chain "A"
d_2	ens_1	chain "B"

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: HIS / End label comp-ID: HIS / Auth seq-ID: 25 - 596 / Label seq-ID: 25 - 596

Dom-ID	Auth asym-ID	Label asym-ID
d_1	A	A
d_2	B	B

NCS oper: (Code: givenMatrix: (0.989891044618, -0.0113878520303, 0.141371979583), (-0.0107746647455, -0.999928934895, -0.00510213277944), (0.141420035301, 0.00352731986242, -0.989943398195)Vector: - ...

#1: Protein	Sialidase domain-containing protein Mass: 67307.703 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Akkermansia muciniphila ATCC BAA-835 (bacteria) Gene: Amuc_1547 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: B2ULI1
#2: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 190 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	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: 2.33 Å³/Da / Density % sol: 47.16 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: Magnesium chloride,Bis-Tris , PEG 3350

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Data collection

Diffraction	Mean temperature: 83 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 20, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 2.04→21.64 Å / Num. obs: 140126 / % possible obs: 97.01 % / Redundancy: 1.9 % / B_iso Wilson estimate: 30.08 Å² / R_pim(I) all: 0.05556 / R_rim(I) all: 0.07858 / Net I/σ(I): 12.75
Reflection shell	Resolution: 2.042→2.115 Å / Num. unique obs: 6090 / CC_1/2: 0.59

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Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
HKL-3000		data reduction
Aimless		data scaling
CRANK2		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.04→21.64 Å / SU ML: 0.2465 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.4116
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2226	3786	2.7 %
R_work	0.1795	136340	-
obs	0.1806	140126	95.64 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 36.05 Å²

Refinement step

Cycle: LAST / Resolution: 2.04→21.64 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9014	0	6	190	9210

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0075	9248
X-RAY DIFFRACTION	f_angle_d	0.9383	12538
X-RAY DIFFRACTION	f_chiral_restr	0.0587	1322
X-RAY DIFFRACTION	f_plane_restr	0.0074	1646
X-RAY DIFFRACTION	f_dihedral_angle_d	5.812	1244

Refine LS restraints NCS

Type: Torsion NCS / Rms dev position: 0.597117125519 Å

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 (%)
2.04-2.07	0.2656	97	0.2881	3559	X-RAY DIFFRACTION	68.7
2.07-2.1	0.3812	127	0.2875	4166	X-RAY DIFFRACTION	78.04
2.1-2.12	0.3008	109	0.2626	4770	X-RAY DIFFRACTION	89.28
2.12-2.15	0.2763	113	0.2458	4768	X-RAY DIFFRACTION	90.94
2.15-2.19	0.2802	132	0.2472	4902	X-RAY DIFFRACTION	91.16
2.19-2.22	0.2992	162	0.2359	4836	X-RAY DIFFRACTION	94.3
2.22-2.26	0.2881	134	0.2324	5021	X-RAY DIFFRACTION	94.29
2.26-2.3	0.2505	157	0.235	5015	X-RAY DIFFRACTION	95.51
2.3-2.34	0.2988	132	0.2315	5117	X-RAY DIFFRACTION	96.68
2.34-2.38	0.299	123	0.2206	5074	X-RAY DIFFRACTION	95.97
2.38-2.43	0.27	167	0.2166	5215	X-RAY DIFFRACTION	98.77
2.43-2.48	0.2938	128	0.2062	5230	X-RAY DIFFRACTION	97.77
2.48-2.54	0.2362	148	0.2087	5232	X-RAY DIFFRACTION	99.93
2.54-2.6	0.2591	153	0.207	5173	X-RAY DIFFRACTION	98.63
2.6-2.67	0.2896	147	0.2066	5333	X-RAY DIFFRACTION	99.89
2.68-2.75	0.2332	140	0.1966	5192	X-RAY DIFFRACTION	98.98
2.75-2.84	0.2534	140	0.2003	5274	X-RAY DIFFRACTION	99.1
2.84-2.94	0.2399	160	0.1944	5230	X-RAY DIFFRACTION	99.93
2.94-3.06	0.2658	152	0.1913	5255	X-RAY DIFFRACTION	99.41
3.06-3.2	0.2783	149	0.1852	5225	X-RAY DIFFRACTION	99.3
3.2-3.37	0.2104	139	0.1793	5276	X-RAY DIFFRACTION	99.54
3.37-3.58	0.2142	141	0.1676	5270	X-RAY DIFFRACTION	99.69
3.58-3.85	0.1883	144	0.151	5276	X-RAY DIFFRACTION	99.69
3.85-4.24	0.1572	147	0.1402	5241	X-RAY DIFFRACTION	99.56
4.24-4.85	0.1633	153	0.1248	5280	X-RAY DIFFRACTION	99.72
4.85-6.08	0.1627	148	0.1382	5214	X-RAY DIFFRACTION	99.26
6.08-21.64	0.1806	144	0.156	5196	X-RAY DIFFRACTION	98.25

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	0.303090688066	-0.0789650797003	0.0839565924218	0.372212962371	-0.289218487624	0.278143608512	-0.00454993943632	-0.0709283331513	-0.0710555098102	0.0349655383686	0.0945130674839	0.049078103405	0.101534166909	-0.0988138428246	0.0155891816418	0.235230769409	-0.0635019500275	-0.0136117758569	0.242351853896	0.0569409171201	0.268215641021	-3.18180653942	-10.6925450041	130.606203226
2	0.11297855854	0.037352881622	0.0579861091265	0.104927139713	0.101402714989	0.0833751277187	-0.013469506498	-0.0172947455921	0.0673227703765	-0.0935184543662	0.0620089900636	0.061209152201	-0.0194507523041	-0.033362287625	1.9278977447E-8	0.227267365117	-0.0351591563906	-0.00462396480023	0.239379916933	0.0361753895791	0.28066315276	-1.72451723266	7.88009565258	117.200459345
3	0.142018541282	0.0215970894879	0.1625117292	-0.0395481086614	0.0291147502729	0.10154507179	0.00697437894544	-0.0241461061802	-0.0518450409674	-0.0609063576547	0.0129584046773	0.0301204372723	-0.0480289835096	0.0304622398728	1.03320289752E-8	0.225597154166	-0.0155798662904	0.0214300235229	0.162087948642	0.0186746239562	0.236142196117	10.8470440827	8.89687308556	120.982369828
4	0.0420825302212	-0.0127665549821	-0.011069592396	0.0555352819562	-0.0635003161201	0.205372377625	-0.0235136319977	-0.017869031924	-0.0681935681525	0.0298216240804	0.0891349141258	0.00860506266256	0.124948328386	-0.0825520312962	3.18579436086E-8	0.229553860379	-0.039585470826	0.00237830577928	0.220025690237	-0.00289418028475	0.260102752159	15.8262107393	3.11731347348	128.70426974
5	0.0487458226958	0.146209030099	0.0354076951913	0.175586589256	-0.0500656284111	0.066363666626	0.00482796922267	-0.0368597129085	-0.0701530645743	0.0222308271702	0.0103466162407	-0.0225551352992	0.0132273348318	-0.0128723317101	-1.7871369724E-8	0.237098458088	-0.0181708641523	0.00928705722255	0.167821316694	0.00602350346854	0.208655737924	19.8033922426	4.24756269352	133.736084119
6	0.22272592109	-0.149344705411	-0.0718505059775	0.174294520498	0.0600285225521	0.0379453677757	0.00515820600844	0.058160898798	-0.054432199848	-0.0143404274391	0.12144657217	-0.0546285193551	0.0191081002659	0.132000570876	2.4071023227E-7	0.254263009562	-0.0355654731726	-0.00802124358691	0.244966198329	-0.0285178568222	0.273420536329	36.8621986734	4.91895307918	121.210426469
7	0.298549636291	0.0243524268279	-0.0192408046115	0.212263743576	0.00750976962366	0.215813306753	0.004117065783	0.0440870962659	0.00812365324494	0.00331223432897	0.0400902739746	-0.0142825197479	-0.0902615828459	0.0586380687438	0.080809731822	0.211832174032	-0.0586370110154	0.00651683820501	0.150377656656	-0.0195276041402	0.215868240042	32.4872154989	22.3892617644	126.586498308
8	0.216561844546	0.204073148569	-0.02417808025	0.144473356211	-0.227536842208	0.636454053059	0.0959924484567	0.198381077676	0.0742843791325	-0.0122671243634	0.0863686448767	-0.224713964038	-0.262222006204	-0.650415606773	0.134383170784	0.235112234085	0.176358359322	-0.00163283518476	0.574009168501	0.0932345493115	0.162033168335	0.471364187983	-3.1576265592	83.6220763831
9	0.269307733135	-0.185920279167	-0.478438875329	0.23307404856	0.100540350021	0.47439485606	0.0303479295726	-0.0468757767855	-0.13072565986	0.164617774758	-0.0713988753046	-0.118295197461	0.266836893422	-0.56887882875	-0.0403424041766	0.198596136339	-0.105660103942	0.0157571786356	0.449778886895	-0.0487069391888	0.20398048231	-0.190869107931	-21.6855204821	97.2492545823
10	0.0732086876259	0.143109513007	-0.191915920599	-0.07270555248	0.29437646622	0.235053475354	-0.0212072973644	0.0209275482592	0.0781455081997	0.0457170326123	-0.0466968649872	-0.0601279844537	0.0543996680995	-0.146718284104	-0.0278010461641	0.204963130731	-0.089885970647	-0.0200817697108	0.220071070992	-0.0131257844164	0.198237727065	14.9984016927	-22.3089128037	92.7582422034
11	0.0702087337485	0.103839432499	-0.0575420219099	0.168852054579	-0.0959152107187	0.143780813085	0.0103397565568	0.0539677393183	0.0716842315369	0.0313045535876	-0.0258645154105	-0.0157279867625	0.00121123227734	-0.142889153383	-3.97503259189E-6	0.264205101823	-0.0411772556542	-0.0157837202223	0.242771444831	-0.00757237341801	0.226191315561	21.7982748353	-16.4494139763	85.1809396391
12	0.233537124318	0.178818576527	0.155793279172	0.121364949766	0.0638475241198	0.0720257660428	0.00621640986324	-0.0669247747377	0.109790524418	-0.0152782470416	0.136303300082	-0.0122408888128	-0.154019509893	0.199641780977	8.13455113406E-8	0.265576870015	-0.0766850707688	0.0178771194222	0.231708602138	-0.0208298057703	0.242193344829	38.456743941	-19.0153393117	98.6631591849
13	0.234384205354	-0.0911430287827	0.0926873536196	0.155498512792	-0.057698422556	0.414200822454	-0.0178714636111	-0.0275930678626	-0.00848751504857	-0.0202471347366	0.0340681176368	-0.00642122344892	0.0744066476393	0.0538677868059	-0.000296258980093	0.225339288565	-0.0502549150949	0.00554778914442	0.162480852185	-0.0218313772668	0.204443389105	34.7744168606	-36.4945799189	92.7187958397

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 156 )	A	B	25 - 156	1 - 132
2	2	chain 'A' and (resid 157 through 250 )	A	B	157 - 250	133 - 226
3	3	chain 'A' and (resid 251 through 313 )	A	B	251 - 313	227 - 289
4	4	chain 'A' and (resid 314 through 355 )	A	B	314 - 355	290 - 331
5	5	chain 'A' and (resid 356 through 409 )	A	B	356 - 409	332 - 385
6	6	chain 'A' and (resid 410 through 456 )	A	B	410 - 456	386 - 432
7	7	chain 'A' and (resid 457 through 596 )	A	B	457 - 596	433 - 572
8	8	chain 'B' and (resid 25 through 157 )	B	C	25 - 157	1 - 133
9	9	chain 'B' and (resid 158 through 250 )	B	C	158 - 250	134 - 226
10	10	chain 'B' and (resid 251 through 339 )	B	C	251 - 339	227 - 315
11	11	chain 'B' and (resid 340 through 409 )	B	C	340 - 409	316 - 385
12	12	chain 'B' and (resid 410 through 456 )	B	C	410 - 456	386 - 432
13	13	chain 'B' and (resid 457 through 596 )	B	C	457 - 596	433 - 572

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