PDB-8u48: Crystal structure of Bacteroides thetaiotamicron BT1285 D161A-E16...

ID or keywords:

Entry

Database: PDB / ID: 8u48

Title

Crystal structure of Bacteroides thetaiotamicron BT1285 D161A-E163A inactive Endoglycosidase in complex with high-mannose N-glycan (Man9GlcNAc2) substrate

Components

Endo-beta-N-acetylglucosaminidase

Keywords

CARBOHYDRATE / Inactive Endoglycosidase / Artificial Lectin / High-Mannose specific / Bacteroides / GH18 family

Function / homology

Function and homology information

mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase activity / carbohydrate metabolic process / extracellular region
Similarity search - Function

Biological species

Bacteroides thetaiotaomicron VPI-5482 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.9 Å

Authors

Sastre, D.E. / Sultana, N. / Navarro, M.V.A.S. / Sundberg, E.J.

Funding support

United States, 1items

Citation

Journal: Nat Commun / Year: 2024
Title: Human gut microbes express functionally distinct endoglycosidases to metabolize the same N-glycan substrate.
Authors: Sastre, D.E. / Sultana, N. / V A S Navarro, M. / Huliciak, M. / Du, J. / Cifuente, J.O. / Flowers, M. / Liu, X. / Lollar, P. / Trastoy, B. / Guerin, M.E. / Sundberg, E.J.

History

Deposition	Sep 9, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 29, 2024	Provider: repository / Type: Initial release
Revision 1.1	Jun 26, 2024	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8u48.cif.gz	235.7 KB	Display	PDBx/mmCIF format
PDB format	pdb8u48.ent.gz	188.4 KB	Display	PDB format
PDBx/mmJSON format	8u48.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8u48_validation.pdf.gz	2.5 MB	Display	wwPDB validaton report
Full document	8u48_full_validation.pdf.gz	2.5 MB	Display
Data in XML	8u48_validation.xml.gz	28.5 KB	Display
Data in CIF	8u48_validation.cif.gz	43.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/u4/8u48 ftp://data.pdbj.org/pub/pdb/validation_reports/u4/8u48	HTTPS FTP

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Related structure data

Related structure data	8u46C 8u47C 8u9fC 8w01C 8w04C 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	#261 - Sep 2021 DNA-Sequencing Nanopores similarity (1) #22 - Oct 2001 Photosystem I similarity (1) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (1) #29 - May 2002 Penicillin-binding Proteins similarity (1) #95 - Nov 2007 Multidrug Resistance Transporters similarity (1)

Deposited unit

A: Endo-beta-N-acetylglucosaminidase

B: Endo-beta-N-acetylglucosaminidase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	56.919, 71.260, 80.487
Angle α, β, γ (deg.)	90.00, 94.63, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein

Endo-beta-N-acetylglucosaminidase

Mass: 30353.545 Da / Num. of mol.: 2 / Mutation: D161A, E163A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Bacteroides thetaiotaomicron VPI-5482 (bacteria)
Gene: BT_1285 / Production host:

Escherichia coli BL21 (bacteria) / References: UniProt: Q8A889

#2: Polysaccharide

alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D- ...

Type: oligosaccharide / Mass: 1883.668 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source

Descriptor	Type	Program
DManpa1-2DManpa1-2DManpa1-3[DManpa1-2DManpa1-3[DManpa1-2DManpa1-6]DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROH	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/3,11,10/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-g1_d2-e1_e2-f1_g3-h1_g6-j1_h2-i1_j2-k1	WURCS	PDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}	LINUCS	PDB-CARE

#3: Chemical

ChemComp-PO4 / PHOSPHATE ION

Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO₄ / Feature type: SUBJECT OF INVESTIGATION

#4: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 645 / 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: 2.67 Å³/Da / Density % sol: 53.97 %
Crystal grow	Temperature: 297 K / Method: vapor diffusion, sitting drop Details: 0.056 M Sodium phosphate monobasic monohydrate, 1.344 M Potassium phosphate dibasic, pH 8.2.

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 10, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.9→50 Å / Num. obs: 49043 / % possible obs: 98.8 % / Redundancy: 4.7 % / CC_1/2: 0.987 / CC star: 0.997 / R_pim(I) all: 0.109 / R_rim(I) all: 0.238 / Net I/σ(I): 18.2
Reflection shell	Resolution: 1.9→1.93 Å / Redundancy: 3.7 % / Num. unique obs: 2458 / CC_1/2: 0.636 / CC star: 0.882 / R_pim(I) all: 0.443 / R_rim(I) all: 0.886 / % possible all: 98.3

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Processing

Software

Name	Version	Classification
PHENIX	(1.20.1_4487: ???)	refinement
HKL-2000		data scaling
HKL-2000		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.9→28.87 Å / SU ML: 0.21 / Cross valid method: NONE / σ(F): 1.38 / Phase error: 22.8 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2219	2526	5.16 %
R_work	0.1888	-	-
obs	0.1905	48955	96.67 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.9→28.87 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4016	0	276	645	4937

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_dihedral_angle_d	12.298	1637
X-RAY DIFFRACTION	f_chiral_restr	0.057	721
X-RAY DIFFRACTION	f_plane_restr	0.005	747

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 (%)
1.9-1.94	0.287	115	0.2239	2020	X-RAY DIFFRACTION	77
1.94-1.98	0.2998	146	0.2238	2640	X-RAY DIFFRACTION	99
1.98-2.02	0.2541	156	0.2152	2573	X-RAY DIFFRACTION	99
2.02-2.07	0.2744	156	0.21	2641	X-RAY DIFFRACTION	99
2.07-2.12	0.2663	150	0.2013	2599	X-RAY DIFFRACTION	98
2.12-2.17	0.2327	164	0.1999	2613	X-RAY DIFFRACTION	99
2.18-2.24	0.2318	154	0.1942	2624	X-RAY DIFFRACTION	99
2.24-2.31	0.2578	134	0.1944	2632	X-RAY DIFFRACTION	99
2.31-2.39	0.2681	124	0.1924	2611	X-RAY DIFFRACTION	98
2.39-2.49	0.2349	142	0.1847	2608	X-RAY DIFFRACTION	98
2.49-2.6	0.2187	127	0.1836	2481	X-RAY DIFFRACTION	93
2.6-2.74	0.2106	148	0.1715	2629	X-RAY DIFFRACTION	99
2.74-2.91	0.2162	133	0.1737	2647	X-RAY DIFFRACTION	100
2.91-3.14	0.2175	139	0.1741	2688	X-RAY DIFFRACTION	100
3.14-3.45	0.1804	137	0.1677	2658	X-RAY DIFFRACTION	99
3.45-3.95	0.1694	144	0.1681	2626	X-RAY DIFFRACTION	98
3.95-4.97	0.2115	127	0.1681	2494	X-RAY DIFFRACTION	92
4.97-28.87	0.2301	130	0.2324	2645	X-RAY DIFFRACTION	96

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	7.8944	-0.1498	-5.3441	3.1241	-1.48	4.419	0.0375	-0.6665	0.445	0.7272	0.028	-0.3807	-0.3646	0.8579	0.0069	0.2258	0.0006	-0.059	0.1827	-0.0212	0.21	4.645	-14.471	13.04
2	1.2936	-0.0293	-0.7214	1.9399	0.1769	2.4512	-0.0305	0.1861	0.0296	-0.1479	0.0566	0.0035	0.0344	0.0686	0.007	0.1903	-0.0103	-0.0086	0.1969	0.0168	0.1646	-1.698	-10.304	-2.817
3	6.1824	-2.0835	-0.5014	6.6162	1.1958	5.6718	-0.0386	-0.75	0.608	0.5542	0.0846	-0.0326	-0.4426	0.4635	0.0311	0.2084	-0.0375	0.0194	0.194	-0.0135	0.1701	0.241	-7.063	11.092
4	1.7381	-0.8747	-0.541	1.7385	1.0028	0.9998	0.0354	0.0125	0.1255	-0.1726	-0.0073	0.0205	-0.0381	0.0987	-0.0539	0.2453	0.0187	0.0348	0.1815	0.0249	0.1642	10.097	-14.047	-12.553
5	2.9499	-1.392	0.0034	5.6732	0.4015	2.9547	0.0633	-0.2326	0.5183	0.064	0.0596	-0.3395	-0.4116	-0.0245	-0.0532	0.18	-0.0129	0.0401	0.1578	-0.0019	0.227	7.343	-4.816	-0.506
6	0.5782	-0.4133	-0.2303	2.0791	0.9207	0.4113	0.0431	0.0208	0.1306	-0.0151	-0.0497	-0.0966	-0.0022	-0.023	0.0048	0.2171	-0.0166	0.0244	0.2204	0.0022	0.1829	16.388	-20.539	-8.234
7	3.0136	1.2083	0.5533	3.9823	1.8425	4.5134	0.0229	-0.1575	0.0492	-0.0615	-0.2119	-0.0121	0.0957	-0.1195	0.1585	0.1225	0.0306	0.0301	0.1264	0.0264	0.1458	19.045	-26.755	-6.41
8	2.1081	-0.348	-0.3979	1.0879	0.0173	1.1436	-0.0989	-0.0929	-0.0635	0.0752	0.0746	0.0915	0.0053	0.051	0.0303	0.1741	-0.0095	0.0043	0.1173	-0.0072	0.123	3.146	-23.464	7.946
9	4.0169	-1.5318	1.5903	4.6512	-2.4531	2.7035	-0.0162	-0.1394	0.3096	0.134	0.0973	-0.2746	-0.1959	0.0207	-0.0626	0.2088	0.0065	0.0559	0.1707	0.0015	0.2042	-8.693	-10.126	11.669
10	6.2454	-5.7178	-5.3032	8.111	6.6802	5.6611	0.5561	0.5744	0.2579	-0.7193	-0.3935	-0.3504	-0.6566	-0.34	-0.1556	0.2618	0.0115	0.0297	0.3054	0.0496	0.2647	-5.206	-3.137	-7.222
11	2.2446	-2.3285	0.1317	6.9536	-1.2697	4.0367	0.0909	0.8753	-0.4051	-0.0403	0.0102	0.2702	-0.007	-0.504	-0.0531	0.16	0.0237	-0.0007	0.192	-0.0492	0.0671	16.506	-35.98	38.479
12	0.6342	0.3015	-0.9377	1.7348	-0.7823	2.0663	-0.0333	0.0445	-0.0409	0.0338	-0.0184	-0.1047	0.1272	0.0439	0.0858	0.1986	0.0114	-0.005	0.1569	-0.0102	0.1511	29.479	-39.453	33.993
13	7.5851	-1.2653	0.305	5.3072	-0.842	3.3352	-0.0252	0.1572	-0.7651	-0.2181	0.0268	0.3551	0.5471	-0.1208	-0.0061	0.2775	-0.017	0.0272	0.1643	-0.02	0.1679	23.737	-47.371	33.335
14	1.1752	0.8019	-0.7199	1.9737	0.2533	1.1631	0.0058	-0.0187	0.0464	-0.1055	-0.0504	0.1165	0.0024	0.0768	0.089	0.1653	0.0009	0.009	0.1261	-0.0132	0.1281	32.116	-24.595	21.965
15	4.6715	3.9153	-3.3785	4.0366	-3.9881	5.4663	-0.1522	-0.2294	-0.2136	-1.0484	-0.1469	-0.2277	0.5351	0.1058	0.2265	0.2718	0.0002	0.0066	0.1993	-0.042	0.1672	28.622	-36.734	17.892
16	3.2375	0.3634	0.151	3.9253	-1.7681	0.9192	0.1701	-0.2845	0.2819	0.1284	0.0469	-0.1478	-0.0073	0.1585	-0.1975	0.299	-0.0073	0.0188	0.2476	-0.0451	0.1897	24.595	-38.473	26.852
17	3.0936	0.6077	-2.4209	2.68	-1.2466	4.0154	0.2011	-0.2677	0.1166	-0.0397	-0.2033	-0.3036	-0.2131	0.3546	-0.0427	0.1958	-0.0255	0.0134	0.1499	0.0128	0.1982	34.813	-18.95	25.538
18	3.0014	3.022	0.896	7.1913	1.6542	2.3851	0.0333	0.1092	-0.1894	0.0207	0.1978	0.1458	0.1829	-0.1892	-0.1578	0.1794	0.0226	-0.0328	0.2258	-0.0041	0.1305	21.171	-28.374	18.316
19	1.1048	0.1059	-0.7498	1.5575	-0.3668	1.9381	0.0142	0.0642	-0.0177	0.1382	0.0761	0.1039	-0.0671	-0.0387	-0.0946	0.1832	0.0109	0.0122	0.1369	-0.016	0.1489	16.732	-26.67	37.155
20	0.9245	-0.0405	0.493	1.7643	-0.7543	0.9459	-0.0447	-0.034	-0.1388	0.1436	0.0358	0.0419	0.0886	0.0233	0.0009	0.2688	-0.0115	0.0501	0.1524	-0.0087	0.1444	19.814	-38.81	46.973

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	( CHAIN A AND RESID 44:49 )	A	44 - 49
2	X-RAY DIFFRACTION	2	( CHAIN A AND RESID 50:65 )	A	50 - 65
3	X-RAY DIFFRACTION	3	( CHAIN A AND RESID 66:75 )	A	66 - 75
4	X-RAY DIFFRACTION	4	( CHAIN A AND RESID 76:105 )	A	76 - 105
5	X-RAY DIFFRACTION	5	( CHAIN A AND RESID 106:123 )	A	106 - 123
6	X-RAY DIFFRACTION	6	( CHAIN A AND RESID 124:166 )	A	124 - 166
7	X-RAY DIFFRACTION	7	( CHAIN A AND RESID 167:193 )	A	167 - 193
8	X-RAY DIFFRACTION	8	( CHAIN A AND RESID 194:277 )	A	194 - 277
9	X-RAY DIFFRACTION	9	( CHAIN A AND RESID 278:299 )	A	278 - 299
10	X-RAY DIFFRACTION	10	( CHAIN A AND RESID 300:306 )	A	300 - 306
11	X-RAY DIFFRACTION	11	( CHAIN B AND RESID 44:52 )	B	44 - 52
12	X-RAY DIFFRACTION	12	( CHAIN B AND RESID 53:105 )	B	53 - 105
13	X-RAY DIFFRACTION	13	( CHAIN B AND RESID 106:121 )	B	106 - 121
14	X-RAY DIFFRACTION	14	( CHAIN B AND RESID 122:140 )	B	122 - 140
15	X-RAY DIFFRACTION	15	( CHAIN B AND RESID 141:153 )	B	141 - 153
16	X-RAY DIFFRACTION	16	( CHAIN B AND RESID 154:161 )	B	154 - 161
17	X-RAY DIFFRACTION	17	( CHAIN B AND RESID 162:177 )	B	162 - 177
18	X-RAY DIFFRACTION	18	( CHAIN B AND RESID 178:192 )	B	178 - 192
19	X-RAY DIFFRACTION	19	( CHAIN B AND RESID 193:260 )	B	193 - 260
20	X-RAY DIFFRACTION	20	( CHAIN B AND RESID 261:306 )	B	261 - 306

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