PDB-8gex: Crystal structure of the ferric enterobactin transporter (XusB) f...

ID or keywords:

Entry

Database: PDB / ID: 8gex

Title

Crystal structure of the ferric enterobactin transporter (XusB) from Bacteroides thetaiotaomicron

Components

DUF4374 domain-containing protein

Keywords

TRANSPORT PROTEIN

Function / homology

Protein of unknown function DUF4374 / Domain of unknown function (DUF4374) / DUF4374 domain-containing protein

Function and homology information

Biological species

Bacteroides thetaiotaomicron (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.55 Å

Authors

Perera, Y.R. / Chazin, W.J.

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	R35GM147470	United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)	#1R01DK134692-01	United States

Citation

Journal: Cell Host Microbe / Year: 2023
Title: Iron acquisition by a commensal bacterium modifies host nutritional immunity during Salmonella infection.
Authors: Spiga, L. / Fansler, R.T. / Perera, Y.R. / Shealy, N.G. / Munneke, M.J. / David, H.E. / Torres, T.P. / Lemoff, A. / Ran, X. / Richardson, K.L. / Pudlo, N. / Martens, E.C. / Folta-Stogniew, E. ...

History

Deposition	Mar 7, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 2, 2023	Provider: repository / Type: Initial release
Revision 1.1	May 22, 2024	Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.2	Aug 14, 2024	Group: Database references / Category: citation / citation_author

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8gex.cif.gz	940.5 KB	Display	PDBx/mmCIF format
PDB format	pdb8gex.ent.gz	789.8 KB	Display	PDB format
PDBx/mmJSON format	8gex.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8gex_validation.pdf.gz	470.4 KB	Display	wwPDB validaton report
Full document	8gex_full_validation.pdf.gz	490.1 KB	Display
Data in XML	8gex_validation.xml.gz	79.3 KB	Display
Data in CIF	8gex_validation.cif.gz	108 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ge/8gex ftp://data.pdbj.org/pub/pdb/validation_reports/ge/8gex	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

Deposited unit

A: DUF4374 domain-containing protein

B: DUF4374 domain-containing protein

C: DUF4374 domain-containing protein

D: DUF4374 domain-containing protein

E: DUF4374 domain-containing protein

F: DUF4374 domain-containing protein

279 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: DUF4374 domain-containing protein

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

2

B: DUF4374 domain-containing protein

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

3

C: DUF4374 domain-containing protein

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

4

D: DUF4374 domain-containing protein

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

5

E: DUF4374 domain-containing protein

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

6

F: DUF4374 domain-containing protein

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

Unit cell

Length a, b, c (Å)	174.193, 174.193, 294.280
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	152
Space group name H-M	P3₁21

#1: Protein	DUF4374 domain-containing protein Mass: 46474.180 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria) Gene: Btheta7330_00980, DW780_15885, GAN91_09105, GAO00_22735, GAO51_09325 Production host: Escherichia coli (E. coli) / References: UniProt: A0A0P0ENH6
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 281 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 4.76 Å³/Da / Density % sol: 74.17 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 2 M ammonium sulfate, 0.1 M sodium cacodylate (pH 6.5), and 0.2 M sodium chloride, and 0.1 M Sodium citrate tribasic dihydrate

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 31, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9786 Å / Relative weight: 1
Reflection	Resolution: 2.55→29.9 Å / Num. obs: 167888 / % possible obs: 99.8 % / Redundancy: 3.8 % / B_iso Wilson estimate: 44.96 Å² / CC_1/2: 0.997 / Net I/σ(I): 15.38
Reflection shell	Resolution: 2.55→2.59 Å / Mean I/σ(I) obs: 2.02 / Num. unique obs: 8360 / CC_1/2: 0.841

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Processing

Software

Name	Version	Classification
PHENIX	(1.20.1_4487: ???)	refinement
HKL-2000		data reduction
Coot	0.9.6	model building
HKL-2000		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.55→29.9 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.03 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.247	8535	5.08 %	RANDOM
R_work	0.224	-	-	-
obs	0.225	167888	99.8 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.55→29.9 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	18781	0	0	281	19062

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	19205
X-RAY DIFFRACTION	f_angle_d	0.488	26120
X-RAY DIFFRACTION	f_dihedral_angle_d	11.698	6723
X-RAY DIFFRACTION	f_chiral_restr	0.044	2892
X-RAY DIFFRACTION	f_plane_restr	0.003	3348

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 (%)
2.55-2.58	0.365	278	0.3308	5197	X-RAY DIFFRACTION	99
2.58-2.61	0.3324	348	0.3089	5204	X-RAY DIFFRACTION	100
2.61-2.64	0.3243	272	0.2973	5281	X-RAY DIFFRACTION	100
2.64-2.67	0.3428	247	0.3054	5315	X-RAY DIFFRACTION	100
2.67-2.71	0.3338	263	0.3008	5249	X-RAY DIFFRACTION	100
2.71-2.75	0.3423	239	0.2885	5295	X-RAY DIFFRACTION	100
2.75-2.78	0.3243	260	0.2806	5298	X-RAY DIFFRACTION	100
2.78-2.83	0.2976	336	0.262	5235	X-RAY DIFFRACTION	100
2.83-2.87	0.2988	271	0.2643	5277	X-RAY DIFFRACTION	100
2.87-2.92	0.2823	283	0.2537	5272	X-RAY DIFFRACTION	100
2.92-2.97	0.33	279	0.2632	5310	X-RAY DIFFRACTION	100
2.97-3.02	0.3032	311	0.2622	5229	X-RAY DIFFRACTION	100
3.02-3.08	0.293	306	0.2543	5259	X-RAY DIFFRACTION	100
3.08-3.14	0.2992	289	0.2423	5286	X-RAY DIFFRACTION	100
3.14-3.21	0.2816	249	0.235	5312	X-RAY DIFFRACTION	100
3.21-3.29	0.2789	309	0.2294	5279	X-RAY DIFFRACTION	100
3.29-3.37	0.2829	263	0.2355	5277	X-RAY DIFFRACTION	100
3.37-3.46	0.2638	277	0.2393	5312	X-RAY DIFFRACTION	100
3.46-3.56	0.2807	295	0.2241	5286	X-RAY DIFFRACTION	100
3.56-3.67	0.2334	225	0.2175	5378	X-RAY DIFFRACTION	100
3.67-3.81	0.2132	266	0.2109	5306	X-RAY DIFFRACTION	100
3.81-3.96	0.2106	302	0.1987	5312	X-RAY DIFFRACTION	100
3.96-4.14	0.1969	294	0.1857	5327	X-RAY DIFFRACTION	100
4.14-4.35	0.1951	285	0.1703	5331	X-RAY DIFFRACTION	100
4.36-4.63	0.1738	311	0.1639	5320	X-RAY DIFFRACTION	100
4.63-4.98	0.1731	313	0.1667	5338	X-RAY DIFFRACTION	100
4.98-5.48	0.2174	293	0.1883	5384	X-RAY DIFFRACTION	100
5.48-6.27	0.2389	294	0.2341	5406	X-RAY DIFFRACTION	100
6.27-7.87	0.2514	295	0.2423	5462	X-RAY DIFFRACTION	100
7.87-29.9	0.2506	282	0.2419	5616	X-RAY DIFFRACTION	99

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	1.6099	-0.3038	-0.1608	1.3207	-0.0567	0.5461	0.0115	0.1105	0.2541	-0.2124	0.0762	-0.1419	-0.0933	0.0819	-0.0815	0.4651	-0.1065	0.1205	0.4047	-0.0078	0.5693	63.925	32.834	30.176
2	1.3236	0.035	0.5683	1.391	0.194	0.6012	-0.1276	-0.0136	-0.4091	-0.0588	0.2336	-0.1464	0.0602	0.0615	-0.0785	0.4805	-0.0194	0.0825	0.4806	-0.0746	0.6845	78.848	12.332	38.619
3	0.7981	0.8756	-0.1139	1.572	0.4207	0.6837	-0.1601	0.0317	-0.3055	-0.0175	0.0554	-0.525	0.2622	0.1835	0.0089	0.5866	0.0182	0.0996	0.546	-0.0535	0.8709	87.364	17.045	34.99
4	1.0322	-0.4265	0.2957	1.5771	-0.5495	0.5995	0.0135	0.174	0.07	-0.0854	-0.0169	-0.6168	0.0251	0.3559	-0.0396	0.5862	-0.0773	0.1912	0.6027	-0.0705	0.8461	86.653	31.885	31.401
5	1.3936	0.5795	0.0605	1.3275	0.4564	0.2726	-0.0763	0.0588	-0.3632	-0.0833	-0.0126	-0.1958	0.257	-0.0519	0.0516	0.4748	-0.107	0.096	0.3933	-0.0192	0.6471	40.161	-1.808	30.875
6	1.4256	0.4514	-0.1168	1.1852	0.1488	0.3189	-0.0387	0.0279	0.0465	-0.2163	0.1084	0.0026	-0.0124	-0.0659	-0.0381	0.5059	-0.0984	0.0728	0.4175	0.0003	0.5368	28.04	13.611	29.691
7	1.1471	0.1128	-0.3344	1.4283	-0.5117	0.4573	-0.0325	-0.1231	0.1145	0.0231	0.0787	0.4244	-0.0075	-0.0448	-0.0576	0.4761	-0.0806	0.0072	0.5443	0.0727	0.6704	7.586	5.071	38.438
8	0.5765	-0.8176	0.1303	1.3494	0.1053	0.6557	-0.1974	0.0157	-0.4673	-0.0658	0.052	0.624	0.1091	-0.1197	0.0928	0.4616	-0.1454	0.0794	0.5281	0.055	0.7348	7.397	-4.65	34.836
9	2.4209	0.8368	-0.8761	1.1246	-0.016	0.4352	-0.1344	-0.0646	-0.6224	0.0656	-0.0686	0.3608	0.2205	-0.3083	0.1335	0.5675	-0.1522	0.0953	0.5338	-0.044	0.755	18.505	-10.994	30.79
10	0.1332	0.011	0.1685	1.105	-0.0268	0.4921	-0.1747	-0.5297	0.8237	0.3896	-0.0062	0.1246	-0.2836	-0.2903	0.0778	0.5599	0.0933	0.0444	0.7493	-0.2306	1.0154	119.138	14.877	73.529
11	2.0334	-0.2635	0.1493	0.9658	-0.0827	0.5378	-0.055	-0.3309	0.1446	0.0918	0.0562	-0.0978	-0.173	-0.0666	-0.0243	0.4997	0.0345	0.0492	0.6473	-0.002	0.7444	120.244	-2.195	66.945
12	1.4567	-0.1326	0.2237	1.5015	-0.3357	0.3477	-0.0236	-0.3483	-0.04	0.0732	0.1669	0.4564	-0.0548	-0.1403	-0.2005	0.4175	0.0579	0.071	0.6644	0.078	0.7733	95.437	-0.303	60.517
13	0.48	0.103	-0.5178	1.1275	-0.3702	1.0912	-0.1183	-0.2781	0.374	0.0754	0.1114	0.3611	-0.113	-0.1001	-0.1422	0.3776	0.0595	0.1095	0.7195	-0.0534	0.8703	94.127	12.883	60.892
14	2.4971	-0.6546	0.8177	0.9246	-0.1291	0.3047	-0.3412	-0.3353	0.4231	-0.0139	0.0193	0.1051	-0.2578	-0.2232	0.2217	0.5852	0.104	0.0557	0.761	-0.1477	0.9668	105.712	19.304	67.267
15	0.8918	0.3134	-0.5129	1.5113	-0.4272	1.2402	-0.0079	-0.1791	0.1875	0.2573	-0.268	0.2288	0.0645	0.0036	0.1432	0.7195	-0.2389	0.2522	0.5064	-0.1681	0.5627	26.299	-37.107	27.584
16	0.5402	0.3288	-0.1728	1.1449	0.1253	0.8336	-0.1179	-0.0006	0.0583	-0.0493	-0.1577	0.5095	0.0246	-0.1511	0.2579	0.664	-0.2159	0.2018	0.5016	-0.1831	0.6717	24.596	-44.209	14.203
17	0.9369	0.3681	-0.429	0.835	0.0839	0.6512	-0.2152	0.1941	-0.2768	-0.506	0.1279	-0.2198	0.0281	0.1222	0.1472	0.7643	-0.2248	0.2695	0.557	-0.0701	0.525	41.699	-45.55	3.092
18	0.4837	-0.0682	-0.1937	0.0297	0.0105	0.6093	-0.0643	-0.0369	-0.091	-0.3135	-0.0554	-0.1931	-0.0016	0.3116	0.0158	0.7989	-0.2909	0.3798	0.5966	-0.0128	0.4287	51.006	-28.757	6.043
19	2.2887	0.9532	-1.1226	1.0174	-0.3003	0.5943	0.3975	-0.1518	0.3293	-0.1806	-0.0854	-0.2543	-0.4491	0.3213	-0.1788	0.7993	-0.2088	0.2105	0.5587	-0.0363	0.5485	40.59	-23.524	14.998
20	1.2809	0.8096	-0.05	1.2167	0.0379	0.1275	0.3604	-0.6033	-0.0894	0.4846	-0.2367	-0.3065	-0.2547	0.2545	-0.0919	0.8911	-0.3314	0.2363	0.749	-0.1073	0.5811	99.123	-14.709	9.218
21	0.9073	0.3269	-0.2709	1.1585	0.1645	1.1688	-0.1136	0.1497	-0.4051	0.0132	-0.001	-0.1293	0.0458	-0.0316	0.084	0.6932	-0.1759	0.3165	0.544	-0.0769	0.7851	87.008	-31.497	-4.015
22	0.7609	-0.3772	-0.004	0.6879	-0.1289	0.6721	-0.046	-0.1906	-0.3149	0.4126	-0.1625	0.139	0.2933	-0.0959	0.0939	0.9186	-0.221	0.3511	0.6281	0.0579	0.8155	74.366	-34.852	12.487
23	1.3916	0.7106	-0.1582	0.5512	-0.0979	0.1382	0.1177	-0.4466	-0.0495	0.362	-0.0179	0.2094	-0.0905	-0.0443	-0.145	1.2662	-0.4292	0.3213	0.8462	0.0608	0.6687	82.672	-25.582	22.025
24	0.2275	0.4629	-0.082	1.2782	0.1533	0.3611	-0.055	0.5616	0.3838	0.0026	0.0098	-0.3505	-0.1238	0.2963	0.2923	0.4046	-0.0292	0.0213	1.0508	0.5814	1.0939	73.276	-38.842	69.291
25	0.7876	0.2442	-0.1846	1.3916	-0.6435	1.5854	-0.0402	0.3343	0.6488	-0.0331	0.0521	-0.0603	-0.0747	0.225	-0.049	0.393	0.0395	0.044	0.9676	0.4789	0.8951	61.946	-40.952	70.431
26	0.4415	-0.1169	-0.0117	0.1653	-0.237	0.4565	-0.0243	0.6679	0.6606	-0.0776	0.1997	0.2618	-0.1591	-0.3468	-0.2259	0.4949	0.0395	0.0736	1.3403	0.6799	0.9649	47.283	-39.324	61.518
27	0.1412	0.1466	-0.1946	0.1534	-0.2116	0.2657	-0.0846	0.4574	0.2185	-0.1404	0.0963	0.0271	-0.0149	0.0129	0.1106	0.6184	-0.0617	0.0344	2.0403	0.9267	0.9977	56.483	-35.246	43.643
28	0.726	0.0773	0.4851	0.4773	0.1738	0.3508	-0.0483	0.4478	0.1186	-0.3212	0.1135	-0.0439	-0.1174	0.0479	0.1961	0.5329	-0.0125	0.0746	1.3474	0.6996	1.0195	74.05	-33.596	53.779

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 41:268 )	A	41 - 268
2	X-RAY DIFFRACTION	2	( CHAIN A AND RESID 269:358 )	A	269 - 358
3	X-RAY DIFFRACTION	3	( CHAIN A AND RESID 359:393 )	A	359 - 393
4	X-RAY DIFFRACTION	4	( CHAIN A AND RESID 394:447 )	A	394 - 447
5	X-RAY DIFFRACTION	5	( CHAIN B AND RESID 41:118 )	B	41 - 118
6	X-RAY DIFFRACTION	6	( CHAIN B AND RESID 122:268 )	B	122 - 268
7	X-RAY DIFFRACTION	7	( CHAIN B AND RESID 269:358 )	B	269 - 358
8	X-RAY DIFFRACTION	8	( CHAIN B AND RESID 359:393 )	B	359 - 393
9	X-RAY DIFFRACTION	9	( CHAIN B AND RESID 394:443 )	B	394 - 443
10	X-RAY DIFFRACTION	10	( CHAIN C AND RESID 41:66 )	C	41 - 66
11	X-RAY DIFFRACTION	11	( CHAIN C AND RESID 67:268 )	C	67 - 268
12	X-RAY DIFFRACTION	12	( CHAIN C AND RESID 269:335 )	C	269 - 335
13	X-RAY DIFFRACTION	13	( CHAIN C AND RESID 336:393 )	C	336 - 393
14	X-RAY DIFFRACTION	14	( CHAIN C AND RESID 394:443 )	C	394 - 443
15	X-RAY DIFFRACTION	15	( CHAIN D AND RESID 41:121 )	D	41 - 121
16	X-RAY DIFFRACTION	16	( CHAIN D AND RESID 122:210 )	D	122 - 210
17	X-RAY DIFFRACTION	17	( CHAIN D AND RESID 211:335 )	D	211 - 335
18	X-RAY DIFFRACTION	18	( CHAIN D AND RESID 336:393 )	D	336 - 393
19	X-RAY DIFFRACTION	19	( CHAIN D AND RESID 394:443 )	D	394 - 443
20	X-RAY DIFFRACTION	20	( CHAIN E AND RESID 41:210 )	E	41 - 210
21	X-RAY DIFFRACTION	21	( CHAIN E AND RESID 211:316 )	E	211 - 316
22	X-RAY DIFFRACTION	22	( CHAIN E AND RESID 317:393 )	E	317 - 393
23	X-RAY DIFFRACTION	23	( CHAIN E AND RESID 394:444 )	E	394 - 444
24	X-RAY DIFFRACTION	24	( CHAIN F AND RESID 41:100 )	F	41 - 100
25	X-RAY DIFFRACTION	25	( CHAIN F AND RESID 101:193 )	F	101 - 193
26	X-RAY DIFFRACTION	26	( CHAIN F AND RESID 194:290 )	F	194 - 290
27	X-RAY DIFFRACTION	27	( CHAIN F AND RESID 291:406 )	F	291 - 406
28	X-RAY DIFFRACTION	28	( CHAIN F AND RESID 407:448 )	F	407 - 448

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