PDB-4mes: Crystal structure of ThiT complexed with LMG116

ID or keywords:

Entry

Database: PDB / ID: 4mes

Title

Crystal structure of ThiT complexed with LMG116

Components

Thiamine transporter ThiT

Keywords

THIAMINE BINDING PROTEIN / S-component / ECF transporter / ABC transporter

Function / homology

Arp2/3 complex 21 kDa subunit ARPC3 - #20 / Arp2/3 complex 21 kDa subunit ARPC3 / Orthogonal Bundle / Mainly Alpha / Chem-26G / DI(HYDROXYETHYL)ETHER / :

Function and homology information

Biological species

Lactococcus lactis subsp. cremoris (lactic acid bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

Swier, L.J.Y.M. / Guskov, A. / Slotboom, D.J.

Citation

Journal: To be Published
Title: Crystal structures of ThiT with small molecule modulators
Authors: Swier, L.J.Y.M. / Gomez, L. / Guskov, A. / Hirsch, A.K.H. / Slotboom, D.J.

History

Deposition	Aug 27, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 27, 2014	Provider: repository / Type: Initial release
Revision 1.1	Jul 29, 2020	Group: Data collection / Derived calculations / Structure summary Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2	Sep 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4mes.cif.gz	171.3 KB	Display	PDBx/mmCIF format
PDB format	pdb4mes.ent.gz	139.1 KB	Display	PDB format
PDBx/mmJSON format	4mes.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/me/4mes ftp://data.pdbj.org/pub/pdb/validation_reports/me/4mes	HTTPS FTP

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Related structure data

Related structure data	3rlbS S: Starting model for refinement
Similar structure data	4n4d-1 3rlb-1 5dju-1 4u9z-d 4pov-1 5djt-d 2ff0-d 5dju-2 4dw7-2 6gp1-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Thiamine transporter ThiT

B: Thiamine transporter ThiT

hetero molecules

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

1

A: Thiamine transporter ThiT

hetero molecules

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

2

B: Thiamine transporter ThiT

hetero molecules

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

Unit cell

Length a, b, c (Å)	61.530, 84.200, 127.210
Angle α, β, γ (deg.)	90.00, 93.52, 90.00
Int Tables number	5
Space group name H-M	C121

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Protein / Sugars , 2 types, 9 molecules AB

#1: Protein

Thiamine transporter ThiT / Thiamine ECF transporter S component ThiT

Mass: 19924.027 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Lactococcus lactis subsp. cremoris (lactic acid bacteria)
Strain: NZ9000 / Gene: LLNZ_01755, thiT / Production host:

Lactococcus lactis (lactic acid bacteria) / Strain (production host): NZ9000 / References: UniProt: D8KFM5

#2: Sugar

ChemComp-BNG / nonyl beta-D-glucopyranoside / Beta-NONYLGLUCOSIDE / nonyl beta-D-glucoside / nonyl D-glucoside / nonyl glucoside

Type: D-saccharide / Mass: 306.395 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Formula: C₁₅H₃₀O₆ / Comment: detergent*YM

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Non-polymers , 7 types, 209 molecules

#3: Chemical	ChemComp-26G / 2-{3-[(4-amino-2-methylpyrimidin-5-yl)methyl]phenyl}ethanol Mass: 243.304 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₄H₁₇N₃O
#4: Chemical	ChemComp-PG4 / TETRAETHYLENE GLYCOL Mass: 194.226 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C₈H₁₈O₅ / Comment: precipitant*YM
#5: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#6: Chemical	ChemComp-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000 Mass: 120.147 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₅H₁₂O₃ / Comment: inhibitor, precipitant*YM
#7: Chemical	ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 Mass: 282.331 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₁₂H₂₆O₇ / Comment: precipitant*YM
#8: Chemical	ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₀H₂₂O₆ / Comment: precipitant*YM
#9: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 169 / 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: 4.13 Å³/Da / Density % sol: 70.2 %
Crystal grow	Temperature: 278 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.15 M ammonium nitrate, 20% PEG3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 278K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.97625 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 9, 2013
Radiation	Monochromator: channel cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97625 Å / Relative weight: 1
Reflection	Resolution: 2→47 Å / Num. all: 43797 / Num. obs: 43725 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Net I/σ(I): 2
Reflection shell	Resolution: 2→2.1 Å / Redundancy: 3.7 % / R_merge(I) obs: 0.86 / Mean I/σ(I) obs: 1.59 / Num. unique all: 5899 / % possible all: 99.9

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Processing

Software

Name	Version	Classification
MxCuBE		data collection
PHASER		phasing
PHENIX	(phenix.refine: 1.8.2_1309)	refinement
XDS		data reduction
XSCALE		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3RLB

3rlb

Resolution: 2→42.323 Å / SU ML: 0.21 / σ(F): 2 / Phase error: 20.59 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2082	2186	5 %	RANDOM
R_work	0.174	-	-	-
obs	0.1758	43721	99.84 %	-
all	-	43797	-	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2→42.323 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2743	0	610	169	3522

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.012	3421
X-RAY DIFFRACTION	f_angle_d	1.314	4462
X-RAY DIFFRACTION	f_dihedral_angle_d	18.975	1350
X-RAY DIFFRACTION	f_chiral_restr	0.074	504
X-RAY DIFFRACTION	f_plane_restr	0.007	456

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 (%)
2-2.0435	0.2844	134	0.272	2544	X-RAY DIFFRACTION	100
2.0435-2.091	0.2876	138	0.2541	2619	X-RAY DIFFRACTION	100
2.091-2.1433	0.2628	134	0.237	2546	X-RAY DIFFRACTION	100
2.1433-2.2013	0.2499	138	0.2303	2624	X-RAY DIFFRACTION	100
2.2013-2.2661	0.2806	137	0.2026	2602	X-RAY DIFFRACTION	100
2.2661-2.3392	0.2201	134	0.1907	2546	X-RAY DIFFRACTION	100
2.3392-2.4228	0.2136	136	0.1772	2586	X-RAY DIFFRACTION	100
2.4228-2.5198	0.2364	136	0.1677	2573	X-RAY DIFFRACTION	100
2.5198-2.6344	0.2179	137	0.1596	2614	X-RAY DIFFRACTION	100
2.6344-2.7733	0.2177	138	0.1546	2621	X-RAY DIFFRACTION	100
2.7733-2.947	0.2015	136	0.1578	2584	X-RAY DIFFRACTION	100
2.947-3.1745	0.1964	137	0.1545	2593	X-RAY DIFFRACTION	100
3.1745-3.4938	0.1875	138	0.1488	2624	X-RAY DIFFRACTION	100
3.4938-3.9991	0.2088	137	0.1558	2603	X-RAY DIFFRACTION	100
3.9991-5.0371	0.1823	136	0.1446	2598	X-RAY DIFFRACTION	100
5.0371-42.3327	0.1804	140	0.1983	2658	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	3.2106	1.7486	-0.9039	7.4969	-5.8808	7.3409	-0.2975	-0.7054	-0.2699	0.3268	-0.0713	-0.8119	0.242	0.8605	0.37	0.2871	0.1455	-0.013	0.5406	0.0056	0.2308	32.5398	3.8292	55.3137
2	3.2608	0.7815	-0.8395	6.0223	-1.4875	4.5487	-0.1142	-0.3951	0.2759	0.7485	0.2401	-0.3417	-0.3878	0.226	-0.0956	0.1294	0.0117	0.0064	0.2386	-0.0523	0.1622	28.7523	12.1252	44.9493
3	3.2904	-1.5775	-0.8957	3.3278	0.7481	5.782	-0.303	-0.5923	-0.0117	0.3682	0.3623	0.1124	-0.2956	0.1349	-0.0411	0.2302	0.0268	0.0396	0.2549	0.0231	0.1578	20.1517	9.7125	52.014
4	3.3862	-4.1212	-4.3244	7.4105	4.6022	8.6735	-0.0928	-0.595	-1.0434	-0.2908	0.1465	0.3803	1.2727	0.5559	0.0086	0.3815	0.1284	0.0726	0.3071	0.0522	0.3758	32.3465	-9.5225	39.013
5	1.4718	-1.1549	0.246	4.3253	-1.3272	1.05	0.4531	0.1914	0.6381	-0.2802	-0.0862	-0.2534	-0.5392	-0.3682	-0.2369	0.2363	0.073	0.0796	0.1882	0.0377	0.2718	17.4449	15.3593	40.0156
6	1.663	-0.1757	-0.1115	3.7481	-1.6021	4.1361	-0.2943	-0.2078	-0.1579	0.2897	0.1056	-0.4252	0.136	0.3975	0.1358	0.1453	0.0051	0.0103	0.1994	-0.0032	0.1893	30.704	6.6424	39.5935
7	5.1853	0.449	-1.0851	6.7127	-4.9365	7.0376	-0.4801	0.9755	0.0284	-0.6754	0.0446	-0.9354	-0.3892	0.2206	0.4143	0.3845	-0.1954	0.0481	0.5523	0.0158	0.2448	36.5848	21.541	7.314
8	6.7305	1.2981	0.4131	7.8722	-4.9261	3.3314	-0.1717	0.7576	-0.7249	-0.0992	0.1036	-0.8195	1.0552	0.1482	0.0975	0.4445	0.0465	0.0484	0.2398	-0.1414	0.3813	30.9133	2.244	20.6763
9	2.187	1.0035	-0.4357	3.0994	-1.0401	1.1305	-0.2519	0.4551	0.0624	-0.4321	0.2158	-0.1867	-0.2044	0.418	0.0618	0.2983	-0.1751	0.0272	0.3313	0.0306	0.2104	30.5476	19.7397	12.02
10	3.9242	2.0498	1.6584	5.6802	4.123	5.3893	-0.1646	0.475	-0.0018	-0.4929	0.0574	0.1229	0.2841	-0.1414	0.1163	0.3584	-0.1417	-0.0084	0.3198	0.0201	0.164	22.3699	12.8971	12.6019
11	6.6314	4.9573	6.2871	6.5182	5.8797	8.5535	0.0472	0.1232	0.7666	-0.1826	0.2674	0.3855	-0.2889	-0.1621	-0.2392	0.3468	-0.1641	0.0285	0.3167	0.0481	0.4267	36.4993	34.5102	23.8258
12	5.1617	4.0069	0.5115	5.1672	0.0039	2.0654	0.0906	-0.1342	0.0184	0.1209	-0.1525	0.0531	0.1014	-0.0623	0.085	0.1232	-0.0663	-0.0168	0.2188	0.0132	0.166	23.106	15.545	23.1881
13	2.7621	2.0915	-0.1272	3.6676	-0.277	1.4292	-0.0585	0.2249	-0.2577	-0.5448	0.1556	-0.0191	0.705	-0.3463	0.0143	0.429	-0.2017	-0.0485	0.2299	0.0149	0.3675	16.8331	-3.4292	24.1685
14	4.3846	1.9637	-1.0744	3.6258	-0.4164	2.6183	-0.0569	0.1495	-0.0351	-0.0254	0.0552	-0.4303	0.0254	0.3251	-0.0219	0.1301	-0.0407	-0.0257	0.2229	0.0341	0.2164	31.3896	12.2162	26.3435
15	2.3966	2.2326	-3.8648	8.7156	-1.9893	6.6434	-0.5165	0.8091	0.1575	-1.374	0.0263	-1.6303	-0.1873	0.9238	0.4972	0.4017	-0.1263	0.0393	0.3975	0.0757	0.4855	43.9572	27.3536	20.0915
16	2.8803	3.517	-0.278	4.6656	-0.5968	0.1932	-0.4895	0.5774	-0.0188	-0.4592	0.2231	0.127	-0.2077	0.1857	0.1019	0.6711	-0.8021	-0.1934	0.3328	0.167	0.4533	41.039	37.0354	13.6236

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 7 through 26 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 27 through 52 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 53 through 98 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 99 through 106 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 107 through 142 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 143 through 182 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 6 through 26 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 27 through 38 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 39 through 69 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 70 through 98 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 99 through 106 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 107 through 132 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 133 through 142 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 143 through 172 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 173 through 177 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 178 through 182 )

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