PDB-7txk: Crystal structure of EgtU solute binding domain from Streptococcu...

ID or keywords:

Entry

Database: PDB / ID: 7txk

Title

Crystal structure of EgtU solute binding domain from Streptococcus pneumoniae D39 in complex with L-ergothioneine

Components

Choline transporter (Glycine betaine transport system permease protein)

Keywords

TRANSPORT PROTEIN / EGT / Soluble binding protein / SBP / ABC transporter

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: 1.78 Å

Authors

Zhang, Y. / Gonzalez-Gutierrez, G. / Giedroc, D.P.

Funding support

United States, 1items

Citation

Journal: Nat Commun / Year: 2022
Title: Discovery and structure of a widespread bacterial ABC transporter specific for ergothioneine.
Authors: Zhang, Y. / Gonzalez-Gutierrez, G. / Legg, K.A. / Walsh, B.J.C. / Pis Diez, C.M. / Edmonds, K.A. / Giedroc, D.P.

History

Deposition	Feb 9, 2022	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 21, 2022	Provider: repository / Type: Initial release
Revision 1.1	Oct 25, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7txk.cif.gz	399.5 KB	Display	PDBx/mmCIF format
PDB format	pdb7txk.ent.gz	275.5 KB	Display	PDB format
PDBx/mmJSON format	7txk.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7txk_validation.pdf.gz	998.2 KB	Display	wwPDB validaton report
Full document	7txk_full_validation.pdf.gz	1001.7 KB	Display
Data in XML	7txk_validation.xml.gz	27.5 KB	Display
Data in CIF	7txk_validation.cif.gz	41 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/tx/7txk ftp://data.pdbj.org/pub/pdb/validation_reports/tx/7txk	HTTPS FTP

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Related structure data

Related structure data	7txlC 4z7eS S: Starting model for refinement 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: Choline transporter (Glycine betaine transport system permease protein)

B: Choline transporter (Glycine betaine transport system permease protein)

hetero molecules

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

1

A: Choline transporter (Glycine betaine transport system permease protein)

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: Choline transporter (Glycine betaine transport system permease protein)

hetero molecules

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

Unit cell

Length a, b, c (Å)	117.999, 129.017, 206.906
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	22
Space group name H-M	F222
Space group name Hall	F22
Symmetry operation	#1: x,y,z #2: x,-y,-z #3: -x,y,-z #4: -x,-y,z #5: x,y+1/2,z+1/2 #6: x,-y+1/2,-z+1/2 #7: -x,y+1/2,-z+1/2 #8: -x,-y+1/2,z+1/2 #9: x+1/2,y,z+1/2 #10: x+1/2,-y,-z+1/2 #11: -x+1/2,y,-z+1/2 #12: -x+1/2,-y,z+1/2 #13: x+1/2,y+1/2,z #14: x+1/2,-y+1/2,-z #15: -x+1/2,y+1/2,-z #16: -x+1/2,-y+1/2,z

Components on special symmetry positions

ID	Model	Components
1	1	A-871- HOH
2	1	A-891- HOH
3	1	A-989- HOH
4	1	B-922- HOH
5	1	B-928- HOH
6	1	B-939- HOH
7	1	B-950- HOH

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Protein , 1 types, 2 molecules AB

#1: Protein	Choline transporter (Glycine betaine transport system permease protein) Mass: 30728.896 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pneumoniae D39 (bacteria) Strain: D39 / NCTC 7466 / Gene: proWX, SPD_1642 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H2ZQB9

#1: Protein

Choline transporter (Glycine betaine transport system permease protein)

Mass: 30728.896 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Streptococcus pneumoniae D39 (bacteria)
Strain: D39 / NCTC 7466 / Gene: proWX, SPD_1642 / Production host:

Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H2ZQB9

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Non-polymers , 5 types, 548 molecules

#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.: 2 / Source method: obtained synthetically / Formula: C₉H₁₆N₃O₂S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-144 / TRIS-HYDROXYMETHYL-METHYL-AMMONIUM Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₂NO₃
#4: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO₄
#5: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 539 / Source method: isolated from a natural source / Formula: H₂O

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Details

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: 3.2 Å³/Da / Density % sol: 61.6 %
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 1.8 - 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: 4.2.2 / Wavelength: 1.07216 Å
Detector	Type: RDI CMOS_8M / Detector: CMOS / Date: Sep 23, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.07216 Å / Relative weight: 1
Reflection	Resolution: 1.78→43.54 Å / Num. obs: 75117 / % possible obs: 99.9 % / Redundancy: 7 % / B_iso Wilson estimate: 25.7 Å² / CC_1/2: 0.998 / R_pim(I) all: 0.033 / R_rim(I) all: 0.087 / R_sym value: 0.081 / Net I/σ(I): 13.7
Reflection shell	Resolution: 1.78→1.82 Å / Redundancy: 7.1 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 4251 / CC_1/2: 0.824 / R_pim(I) all: 0.4 / R_rim(I) all: 1.062 / R_sym value: 0.983 / % possible all: 100

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4Z7E

4z7e

Resolution: 1.78→43.54 Å / SU ML: 0.1644 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.4183
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.1862	3794	5.06 %
R_work	0.1586	71214	-
obs	0.16	75008	99.76 %

Solvent computation

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

Displacement parameters

B_iso mean: 35.41 Å²

Refinement step

Cycle: LAST / Resolution: 1.78→43.54 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4256	0	67	539	4862

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	4392
X-RAY DIFFRACTION	f_angle_d	0.9151	5942
X-RAY DIFFRACTION	f_chiral_restr	0.0491	659
X-RAY DIFFRACTION	f_plane_restr	0.007	768
X-RAY DIFFRACTION	f_dihedral_angle_d	7.7065	589

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 (%)
1.78-1.8	0.3071	132	0.2528	2599	X-RAY DIFFRACTION	99.64
1.8-1.83	0.2592	147	0.2325	2632	X-RAY DIFFRACTION	99.64
1.83-1.85	0.223	111	0.2168	2627	X-RAY DIFFRACTION	99.71
1.85-1.88	0.2587	111	0.2183	2634	X-RAY DIFFRACTION	99.64
1.88-1.91	0.277	166	0.256	2614	X-RAY DIFFRACTION	99.43
1.91-1.94	0.272	114	0.2338	2625	X-RAY DIFFRACTION	99.42
1.94-1.97	0.2357	160	0.2011	2597	X-RAY DIFFRACTION	99.86
1.97-2	0.2016	150	0.183	2606	X-RAY DIFFRACTION	99.93
2-2.04	0.213	136	0.1773	2628	X-RAY DIFFRACTION	99.86
2.04-2.08	0.1986	134	0.1875	2601	X-RAY DIFFRACTION	99.24
2.08-2.12	0.1952	150	0.1534	2626	X-RAY DIFFRACTION	99.89
2.12-2.17	0.1768	118	0.1498	2638	X-RAY DIFFRACTION	99.96
2.17-2.22	0.2035	154	0.1505	2608	X-RAY DIFFRACTION	100
2.22-2.27	0.1914	129	0.1663	2647	X-RAY DIFFRACTION	99.61
2.27-2.33	0.1681	143	0.1475	2629	X-RAY DIFFRACTION	99.96
2.33-2.4	0.1597	144	0.144	2616	X-RAY DIFFRACTION	99.96
2.4-2.48	0.1768	130	0.1503	2654	X-RAY DIFFRACTION	100
2.48-2.57	0.2329	150	0.1641	2634	X-RAY DIFFRACTION	99.96
2.57-2.67	0.1957	144	0.1592	2627	X-RAY DIFFRACTION	100
2.67-2.79	0.1687	139	0.1564	2654	X-RAY DIFFRACTION	100
2.79-2.94	0.2002	151	0.1734	2637	X-RAY DIFFRACTION	99.96
2.94-3.12	0.2131	166	0.1729	2654	X-RAY DIFFRACTION	99.96
3.12-3.36	0.2037	138	0.1593	2650	X-RAY DIFFRACTION	99.96
3.36-3.7	0.1694	133	0.136	2662	X-RAY DIFFRACTION	99.82
3.7-4.24	0.1492	157	0.1228	2673	X-RAY DIFFRACTION	99.96
4.24-5.34	0.1408	146	0.1218	2688	X-RAY DIFFRACTION	99.86
5.34-43.54	0.1821	141	0.1799	2754	X-RAY DIFFRACTION	98.27

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	3.02918981265	0.0557714638957	1.89200769035	4.47684505387	0.522477911182	3.94190938962	-0.063635832075	-0.414884586946	0.101599612012	0.567382838196	-0.0653771101619	0.226795560479	-0.079084036182	-0.210242802592	0.0906373264012	0.289367171372	0.0578617854234	0.0126261480729	0.15994749329	-0.000317087417321	0.192435843146	25.447153613	42.6287071249	108.102416108
2	1.17758389595	0.203427392218	-0.0929295757511	1.98944021153	-0.628680161035	2.59640641117	-0.0108132208017	0.0658653961853	0.132260039894	0.107702519045	0.0117547156871	0.131335166445	-0.217095938	-0.147471971175	-0.00194213199307	0.229835570827	0.0810693246937	0.000870270629431	0.178685670897	-0.0140525946317	0.213722072142	21.1442445551	48.9065008439	94.526562525
3	3.49386173624	-0.613679822922	-1.26293957019	2.74721070391	-0.563863071751	4.16306047629	0.105160513851	0.394182547467	0.182813702666	-0.296027142262	-0.209046528694	-0.776840529589	-0.133680689202	0.738143098635	0.189435624371	0.276255057806	0.0272579089466	0.0999401710102	0.415914658236	0.122684248423	0.412313876408	45.9279841664	47.7771324088	76.3616198814
4	0.993176700691	-0.421426943962	-0.375956566127	1.83559660428	-0.319232396475	2.68018596444	0.0384474731508	0.10025277626	0.0568598817305	-0.0831627237715	-0.148125522031	-0.214827540747	-0.0633049654601	0.230625177699	0.0770470506126	0.171661067506	0.0431171190512	-0.00399438521958	0.196666626956	0.0392102890505	0.227405784872	33.3012540445	45.5315832737	87.6594036194
5	4.04436719325	-0.308481624104	-1.82032262027	3.9077753718	1.44636700505	2.84730115064	-0.105147624534	-0.363898692756	0.288431057695	0.593045950554	-0.045618578852	-0.379288927517	-0.0336191639514	0.768438319541	0.15012070972	0.34382960487	0.00165173953866	-0.123143702047	0.370505235414	0.00837051468777	0.30711184035	39.8347801305	45.6934076584	106.486288066
6	1.86142373639	-0.111311614517	-0.434434184086	2.52769023503	0.319046082089	4.92792969858	-0.130521553129	0.52146284775	-0.16018653335	-0.279414797612	-0.0811677373415	0.169349309329	0.169565210106	-0.669934708797	0.225910838179	0.184341587795	0.000943190965933	0.0046334894146	0.420262833591	-0.0694823330822	0.205499935194	7.26487522816	55.7805522167	52.9542282363
7	3.39329401709	-0.240322813287	1.04834492108	2.77582639892	-0.379059180991	3.22011363461	-0.111252781351	0.0759887219243	-0.245163472131	0.0811809630777	-0.0390305068393	-0.205376534844	0.287196140702	0.139125548138	0.140019424304	0.209354192309	0.066768059738	0.0650113039396	0.220040340015	0.0169586889687	0.218622577442	20.3910019364	53.1895005751	64.3290461096
8	3.56875609461	-1.03771931535	1.26689489412	8.19365460422	1.40291922934	6.23434646098	0.0135086011461	0.00486977555364	1.00484393859	0.302149902409	-0.104104372209	-0.126504853966	-0.915981072432	0.27656458806	0.0257801435019	0.35250547802	-0.0616126760026	-0.00309894601489	0.18059251587	-0.0135612613289	0.442391648237	17.7246290718	79.2395187358	77.2284352446
9	3.9525170234	0.741746462044	0.936059883382	1.88093677752	0.712243482735	3.36710654984	-0.128688103276	-0.371420421172	0.201696864041	0.219041949979	0.00639882605988	-0.10717742659	-0.215535443143	-0.133464555445	0.0729488094565	0.227867110227	0.0684437862351	-0.0213152676213	0.212981000573	-0.0190146862639	0.169677824508	12.3405889422	66.93405423	79.1080138255
10	2.89555552355	-0.41166174857	-0.52363438591	2.35852917486	0.688348125752	2.94209121509	-0.010409612841	0.111763634244	0.583827882123	-0.0355911149489	-0.0158776663622	-0.11163272879	-0.441779437631	-0.0475712735118	0.0517953453447	0.23825260191	0.0182824485287	-0.0364368024655	0.156662437209	0.0345156892522	0.276090720918	12.290778208	73.0104733668	70.9899697444
11	2.38929182508	0.582740522008	0.23373465036	4.49182540247	1.21740769593	4.09201649797	-0.124937939137	0.550375333656	-0.482663195809	-0.370499727497	0.00296754339768	-0.38484969967	0.494946541398	0.0325989752527	0.0974317764894	0.289342544811	0.0422670164465	0.0847836662484	0.351075003149	-0.0639634943244	0.260779608634	17.5018060112	50.5955185871	50.321976087
12	3.2840545683	-0.492670471037	-0.802257958078	4.5158995336	2.74609716981	3.90114605174	0.0828193427448	0.809493265179	0.381432767424	-0.937126827419	-0.215652822879	-0.0549159142811	-0.724424981412	-0.36936705357	0.099009408084	0.529872210902	0.0720609118954	0.0112170032074	0.453825418638	0.16008650419	0.297552718107	14.2614312011	70.9689775187	48.3593226336

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 261 )	A	A	232 - 261	1 - 30
2	2	chain 'A' and (resid 262 through 340 )	A	A	262 - 340	31 - 109
3	3	chain 'A' and (resid 341 through 364 )	A	A	341 - 364	110 - 133
4	4	chain 'A' and (resid 365 through 472 )	A	A	365 - 472	134 - 241
5	5	chain 'A' and (resid 473 through 503 )	A	A	473 - 503	242 - 272
6	6	chain 'B' and (resid 235 through 289 )	B	D	235 - 289	1 - 55
7	7	chain 'B' and (resid 290 through 340 )	B	D	290 - 340	56 - 106
8	8	chain 'B' and (resid 341 through 363 )	B	D	341 - 363	107 - 129
9	9	chain 'B' and (resid 364 through 390 )	B	D	364 - 390	130 - 156
10	10	chain 'B' and (resid 391 through 444 )	B	D	391 - 444	157 - 210
11	11	chain 'B' and (resid 445 through 472 )	B	D	445 - 472	211 - 238
12	12	chain 'B' and (resid 473 through 503 )	B	D	473 - 503	239 - 269

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-Feb 9, 2022. New format data for meta-information of EMDB entries

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