PDB-9egj: Crystal Structure of EgtUC binding domain mutant I243P bound to L...

ID or keywords:

Entry

Database: PDB / ID: 9egj

Title

Crystal Structure of EgtUC binding domain mutant I243P bound to L-Ergothioneine from S. pneumoniae

Components

Ergothioneine transporter EgtUC

Keywords

TRANSPORT PROTEIN / L-ergothioneine / ABC transporter / S. pneumoniae

Function / homology

Function and homology information

ABC-type quaternary ammonium compound transporting activity / quaternary ammonium group transport / glycine betaine transport / amino acid transport / ATP-binding cassette (ABC) transporter complex
Similarity search - Function

Biological species

Streptococcus pneumoniae D39 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.89 Å

Authors

Legg, K.A. / Gonzalez-Gutierrez, G. / Giedroc, D.P.

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: C-H...S hydrogen bonds are essential for molecular recognition of ergothioneine by the bacterial ergothioneine transporter EgtUC in Streptococcus pneumoniae.
Authors: Legg, K.A. / Gonzalez-Gutierrez, G. / Edmonds, K.A. / Shushkov, D.P. / Giedroc, D.P.

History

Deposition	Nov 21, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 26, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9egj.cif.gz	566.2 KB	Display	PDBx/mmCIF format
PDB format	pdb9egj.ent.gz	388.6 KB	Display	PDB format
PDBx/mmJSON format	9egj.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9egj_validation.pdf.gz	1.5 MB	Display	wwPDB validaton report
Full document	9egj_full_validation.pdf.gz	1.5 MB	Display
Data in XML	9egj_validation.xml.gz	66.8 KB	Display
Data in CIF	9egj_validation.cif.gz	92.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/eg/9egj ftp://data.pdbj.org/pub/pdb/validation_reports/eg/9egj	HTTPS FTP

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Related structure data

Related structure data	9eghC 9egiC 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

Deposited unit

A: Ergothioneine transporter EgtUC

B: Ergothioneine transporter EgtUC

C: Ergothioneine transporter EgtUC

D: Ergothioneine transporter EgtUC

hetero molecules

125 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Ergothioneine transporter EgtUC

hetero molecules

defined by author
Evidence: gel filtration
31.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Ergothioneine transporter EgtUC

hetero molecules

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

3

C: Ergothioneine transporter EgtUC

hetero molecules

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

4

D: Ergothioneine transporter EgtUC

hetero molecules

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

Unit cell

Length a, b, c (Å)	119.752, 209.428, 87.975
Angle α, β, γ (deg.)	90.000, 132.880, 90.000
Int Tables number	5
Space group name H-M	C121
Space group name Hall	C2y
Symmetry operation	#1: x,y,z #2: -x,y,-z #3: x+1/2,y+1/2,z #4: -x+1/2,y+1/2,-z

Components on special symmetry positions

ID	Model	Components
1	1	A-602- SO4
2	1	C-602- SO4
3	1	D-602- SO4
4	1	A-816- HOH
5	1	A-887- HOH
6	1	A-1036- HOH
7	1	B-931- HOH
8	1	B-986- HOH
9	1	B-1011- HOH
10	1	C-830- HOH
11	1	C-874- HOH
12	1	C-1015- HOH
13	1	D-720- HOH
14	1	D-901- HOH

#1: Protein	Ergothioneine transporter EgtUC Mass: 31052.309 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pneumoniae D39 (bacteria) Gene: egtUBC, proWX, SPD_1642 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H2ZQB9
#2: Chemical	ChemComp-LW8 / trimethyl-[(2S)-1-oxidanyl-1-oxidanylidene-3-(2-sulfanylidene-1,3-dihydroimidazol-4-yl)propan-2-yl]azanium Mass: 230.307 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₉H₁₆N₃O₂S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1384 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
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: 3.25 Å³/Da / Density % sol: 62.2 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: Sodium citrate tribasic pH 5.6, Potassium Sodium Tartrate 0.2 M and Ammonium Sulphate 1.6 - 2.0 M

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.00002 Å
Detector	Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jun 28, 2024
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.00002 Å / Relative weight: 1
Reflection	Resolution: 1.89→64.47 Å / Num. obs: 124653 / % possible obs: 99.3 % / Redundancy: 3.4 % / B_iso Wilson estimate: 29.71 Å² / CC_1/2: 0.999 / R_pim(I) all: 0.039 / R_rim(I) all: 0.072 / R_sym value: 0.061 / Net I/σ(I): 13.1
Reflection shell	Resolution: 1.89→1.93 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 6288 / CC_1/2: 0.561 / R_pim(I) all: 0.57 / R_rim(I) all: 1.069 / R_sym value: 0.901 / % possible all: 99.8

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Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.89→64.47 Å / SU ML: 0.2802 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.9832
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2542	6362	5.11 %
R_work	0.2137	118218	-
obs	0.2157	124580	99.21 %

Solvent computation

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

Displacement parameters

B_iso mean: 36.32 Å²

Refinement step

Cycle: LAST / Resolution: 1.89→64.47 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8627	0	75	1384	10086

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0049	8855
X-RAY DIFFRACTION	f_angle_d	0.7683	11972
X-RAY DIFFRACTION	f_chiral_restr	0.0481	1328
X-RAY DIFFRACTION	f_plane_restr	0.0056	1555
X-RAY DIFFRACTION	f_dihedral_angle_d	7.3054	1184

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 (%)
1.89-1.92	0.394	182	0.3504	4003	X-RAY DIFFRACTION	99.6
1.92-1.94	0.3354	246	0.303	3864	X-RAY DIFFRACTION	99.66
1.94-1.96	0.3312	221	0.2799	3957	X-RAY DIFFRACTION	99.71
1.96-1.99	0.3164	196	0.2721	3959	X-RAY DIFFRACTION	99.83
1.99-2.01	0.2845	214	0.2665	3957	X-RAY DIFFRACTION	99.67
2.01-2.04	0.3005	210	0.26	3982	X-RAY DIFFRACTION	99.74
2.04-2.07	0.273	192	0.2522	3941	X-RAY DIFFRACTION	99.59
2.07-2.1	0.2912	205	0.2491	3983	X-RAY DIFFRACTION	99.41
2.1-2.13	0.2808	198	0.245	3894	X-RAY DIFFRACTION	99.34
2.13-2.17	0.2814	212	0.2467	3930	X-RAY DIFFRACTION	98.81
2.17-2.2	0.2919	208	0.2426	3917	X-RAY DIFFRACTION	97.4
2.2-2.24	0.2867	226	0.2375	3916	X-RAY DIFFRACTION	99.86
2.24-2.29	0.2764	241	0.226	3905	X-RAY DIFFRACTION	99.76
2.29-2.33	0.3014	202	0.2254	3958	X-RAY DIFFRACTION	99.86
2.33-2.39	0.2417	238	0.228	4002	X-RAY DIFFRACTION	99.86
2.39-2.44	0.319	216	0.2296	3932	X-RAY DIFFRACTION	99.78
2.44-2.5	0.2897	197	0.2294	3972	X-RAY DIFFRACTION	99.71
2.5-2.57	0.2836	232	0.2248	3923	X-RAY DIFFRACTION	99.74
2.57-2.65	0.2671	229	0.2222	3939	X-RAY DIFFRACTION	99.52
2.65-2.73	0.3052	205	0.2219	3961	X-RAY DIFFRACTION	99.43
2.73-2.83	0.2706	209	0.2369	3935	X-RAY DIFFRACTION	99.33
2.83-2.94	0.252	229	0.2234	3968	X-RAY DIFFRACTION	99.13
2.94-3.08	0.2584	242	0.2248	3843	X-RAY DIFFRACTION	98.6
3.08-3.24	0.2607	216	0.2067	3907	X-RAY DIFFRACTION	97.54
3.24-3.44	0.226	219	0.2022	3913	X-RAY DIFFRACTION	99.35
3.44-3.71	0.2223	206	0.1882	3919	X-RAY DIFFRACTION	98.78
3.71-4.08	0.2298	216	0.1863	3952	X-RAY DIFFRACTION	98.79
4.08-4.67	0.2095	183	0.1761	3946	X-RAY DIFFRACTION	98.52
4.67-5.88	0.2179	164	0.1954	3965	X-RAY DIFFRACTION	97.87
5.88-64.47	0.2148	208	0.1874	3975	X-RAY DIFFRACTION	98.42

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	2.42985472972	-0.431223161011	0.580154237382	2.65131160548	-0.421744542365	3.21639718145	0.0430750651629	-0.127090232565	0.0719749858882	0.240394496864	-0.00831741198895	-0.247890780835	-0.209847510332	0.29139931636	-0.0264923989549	0.213399201461	-0.0208739704806	-0.0562408361476	0.23823532924	-0.053592772222	0.178607789588	-52.4701402062	-7.39616144143	14.8827733038
2	2.0407600464	1.72329416053	-0.0891063536262	5.47888630716	0.0719057755159	2.42630767816	0.0483051756188	0.0948383224954	-0.189635847752	0.137700398132	0.15666420907	0.538416526265	0.252956785656	-0.203036224309	-0.15489310106	0.212945510781	-0.0160865831612	-0.0570209734886	0.231879719433	0.0268992538084	0.288895207289	-69.6448193755	-27.3805258468	10.5623436413
3	2.62269487873	1.8758383255	0.944874637367	5.98593752305	-0.27114150286	2.55358895755	0.0815401966254	0.0949139074547	0.40396082066	-0.0213427653778	0.176378700241	1.52338631552	-0.0902613039805	-0.754207114587	-0.0737200098001	0.263417957889	0.0333399419517	-0.0175893553254	0.349184418597	0.0717751417355	0.458691167107	-75.9747444201	-15.5739735165	12.6487862601
4	1.84472702637	1.67679308063	0.162603680866	5.02928677378	0.199274588092	1.45911268271	0.100255830676	-0.182437618032	0.259356068482	0.385064424357	-0.0490680593	0.389937584059	-0.27855134269	0.021670454133	-0.0725185476027	0.300877482533	0.0388545752903	-0.00604431935213	0.268630746757	-0.0464516555169	0.199754258515	-61.4585248701	-2.97355222695	17.4564676903
5	2.37184793087	0.69782061152	0.574148885048	5.20620461076	0.099393512166	3.72719348589	-0.138156513252	0.235568488418	-0.654898517679	-0.381045162902	0.394707160558	-0.295353991126	0.297577320474	0.148026970648	-0.272267839737	0.182357092324	-0.0282404878265	-0.0433303026642	0.234272515422	-0.0525794862453	0.375885386226	-37.2421535278	-53.6531589482	23.4046133187
6	3.45214674529	-1.88382730148	0.010639516472	2.74679058804	0.0910255741187	2.01250267803	-0.327427915078	0.331351704786	0.163279376631	-0.178004189883	0.21266196059	0.237293301912	-0.265895653595	-0.122790300496	0.11442292274	0.260060490724	-0.0893240212264	-0.111896075657	0.25425876165	0.048895079267	0.258756177375	-50.4614388396	-39.6854038932	20.1487244005
7	2.65948707872	0.469399438379	0.520176344386	3.20698490849	1.27795862237	2.5576671763	-0.16259655271	-0.427776729023	0.137565206561	0.23390609706	0.107642073987	0.249994922574	-0.176334699276	-0.220830497636	0.0499586924244	0.18714912438	0.0542702686536	-0.0189558429304	0.24146111416	0.0155663387975	0.216951568193	-44.09257041	-33.0511125823	38.8515538659
8	2.53614414552	0.18712606751	-1.24755082781	2.46946061408	-0.11748190775	3.53047247097	-0.0678308146364	-0.0606945155693	-0.69047787596	0.165344285244	0.107870482652	0.106394579296	0.735580428123	-0.0989548816504	-0.033843107514	0.271390745726	-0.0214066234416	-0.0631448278044	0.22897145023	0.0506575549069	0.467102629359	-45.9470445136	-57.3058972504	29.6011727059
9	3.83774319184	-1.07020156033	0.113364402745	3.72175887747	0.140244030828	3.02973797105	0.095809731218	0.0589052790822	-0.220051201165	-0.0707368432609	0.0135911272309	0.11758187516	0.347435698124	-0.353557034703	-0.115372317918	0.256465538932	-0.0243207551371	0.0375925198155	0.222415192962	0.0210143174724	0.130023909645	-66.3074923303	-106.824654105	8.58943354648
10	3.34669753016	-0.695484231037	-1.08648864058	2.57317954901	1.1428071177	1.4806720912	0.0684291353725	-0.332880972564	0.241490226735	0.578611527368	0.0610632824286	0.232100143248	0.0301185127297	-0.32394835896	-0.109582519349	0.379085568153	0.0136088619955	0.113092329014	0.314989297507	0.0337572841435	0.205672264387	-67.8041569327	-94.8256088605	21.5785714709
11	2.19903517763	1.22662234787	0.093518496316	3.75168644653	0.419947170443	3.59214257185	-0.0250431194742	-0.0129951471296	0.378205094988	-0.0699300137816	0.171461646044	-0.514146217217	-0.218289728283	0.493091772076	-0.124739230553	0.189677814032	-0.0322950048675	0.0496356094335	0.22005433227	-0.0522445155918	0.328081834258	-50.10747465	-81.3902766381	10.5624930367
12	3.28477836042	1.70185982128	-0.527827497556	3.85481487587	0.239968695298	2.87469133391	0.00153234049543	-0.433629067822	0.164536856714	0.401893597709	0.0750440869258	-0.122349674703	0.181832110162	0.177501476222	-0.0859279901957	0.25994119276	0.0761292923381	-0.0012043544668	0.220466428926	0.00383379730679	0.140309948584	-57.1196912225	-94.3868939725	17.2403281443
13	2.79947573698	0.831771460582	0.131490108538	3.29026378929	-0.317325560837	3.06606957263	0.0572550619787	-0.423555326863	-0.432738063344	0.399250241754	-0.114734954001	-0.328090184078	0.544121733732	0.120789457612	0.0221018913234	0.397027866893	0.0456966425357	-0.0163091848842	0.206690975219	0.0429905186549	0.282736270126	-57.9007127625	-108.146762544	18.4869807811
14	3.10714866667	1.69604703082	-0.562712184411	5.81845250992	-1.92187180435	5.99103120645	-0.0404549712699	-0.18541863546	-0.589015657906	-0.257849300259	0.0398855538958	-1.1824339077	0.970728181464	0.371558468807	0.119578380441	0.4379393313	0.143420246376	-0.0229790854464	0.292826717859	0.00370710976823	0.482755712426	-51.7930241407	-114.763160943	13.4612453772
15	3.07695368195	0.578239133191	-0.769918826716	8.23688819012	-1.3452936889	4.14668195722	0.0376195792441	0.243272215396	0.859980731195	-0.367408949682	0.211537078521	0.291752825988	-0.431019026786	-0.148947486938	-0.266886977149	0.188501845915	-0.0278979695338	0.0189728538121	0.242546211238	0.0311801244686	0.39124800539	-81.7677770658	-51.9635844458	25.2535402088
16	2.72653077921	0.413266264155	-0.546595237684	2.58881983932	-0.911835969379	2.1397104948	-0.184320882072	-0.17783845366	-0.0213321938399	0.0248472531446	0.153960185093	-0.208963542264	0.149595854464	0.168717178162	0.0340508855876	0.172546185833	0.0143646311007	0.0166314790776	0.171473305878	-0.0596880191268	0.204038976329	-74.9439216075	-73.2867645485	32.9181759878
17	2.78548658987	0.490640530656	0.490249227159	3.81544103451	0.20694042271	2.821368345	-0.12426153872	0.0289714647277	0.759901920075	0.0195911741743	0.0677965454157	-0.158102610133	-0.703782400835	0.126835374235	0.0531679423906	0.272949731183	-0.0472235095523	0.0121986866855	0.224293422807	-0.0109294547302	0.451475701429	-73.7221430143	-51.3979695154	29.680025464

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 232 through 340 )	A	A	232 - 340	1 - 109
2	2	chain 'A' and (resid 341 through 419 )	A	A	341 - 419	110 - 188
3	3	chain 'A' and (resid 420 through 432 )	A	A	420 - 432	189 - 201
4	4	chain 'A' and (resid 433 through 506 )	A	A	433 - 506	202 - 275
5	5	chain 'B' and (resid 233 through 288 )	B	C	233 - 288	1 - 56
6	6	chain 'B' and (resid 289 through 327 )	B	C	289 - 327	57 - 95
7	7	chain 'B' and (resid 328 through 444 )	B	C	328 - 444	96 - 212
8	8	chain 'B' and (resid 445 through 506 )	B	C	445 - 506	213 - 274
9	9	chain 'C' and (resid 234 through 288 )	C	E	234 - 288	1 - 55
10	10	chain 'C' and (resid 289 through 340 )	C	E	289 - 340	56 - 107
11	11	chain 'C' and (resid 341 through 419 )	C	E	341 - 419	108 - 186
12	12	chain 'C' and (resid 420 through 456 )	C	E	420 - 456	187 - 223
13	13	chain 'C' and (resid 457 through 484 )	C	E	457 - 484	224 - 251
14	14	chain 'C' and (resid 485 through 506 )	C	E	485 - 506	252 - 273
15	15	chain 'D' and (resid 233 through 274 )	D	G	233 - 274	1 - 42
16	16	chain 'D' and (resid 275 through 444 )	D	G	275 - 444	43 - 212
17	17	chain 'D' and (resid 445 through 506 )	D	G	445 - 506	213 - 274

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