PDB-4doj: Crystal structure of BetP in outward-facing conformation

ID or keywords:

Entry

Database: PDB / ID: 4doj

Title

Crystal structure of BetP in outward-facing conformation

Components

Glycine betaine transporter BetP

Keywords

TRANSPORT PROTEIN

Function / homology

Function and homology information

nitrogen compound transport /

symporter activity / identical protein binding /

metal ion binding /

plasma membrane
Similarity search - Function

Biological species

Corynebacterium glutamicum (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 3.25 Å

Authors

Perez, C. / Ziegler, C.

Citation

Journal: Nature / Year: 2012
Title: Alternating-access mechanism in conformationally asymmetric trimers of the betaine transporter BetP.
Authors: Perez, C. / Koshy, C. / Yildiz, O. / Ziegler, C.

History

Deposition	Feb 9, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 6, 2012	Provider: repository / Type: Initial release
Revision 1.1	Sep 12, 2012	Group: Database references
Revision 1.2	Dec 5, 2012	Group: Database references
Revision 1.3	Feb 28, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4doj.cif.gz	603.3 KB	Display	PDBx/mmCIF format
PDB format	pdb4doj.ent.gz	500.8 KB	Display	PDB format
PDBx/mmJSON format	4doj.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

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

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Related structure data

Related structure data	4ainC C: citing same article (ref.)
Similar structure data	2wit-d 4llh-d 4ain-d 4we3-d 21876 5oju-1 3p03-d 6zrx-d Search similar-shape structures by Omokage search (details) 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: Glycine betaine transporter BetP

B: Glycine betaine transporter BetP

C: Glycine betaine transporter BetP

hetero molecules

185 kDa, 3 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)	117.440, 129.320, 184.860
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Glycine betaine transporter BetP Mass: 61234.609 Da / Num. of mol.: 3 / Fragment: unp residues 30-595 / Mutation: G153D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Corynebacterium glutamicum (bacteria) / Gene: betP, Cgl0892, cg1016 / Plasmid: pASK-IBA7 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alfa / References: UniProt: P54582
#2: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical	ChemComp-PGT / (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE / PHOSPHATIDYLGLYCEROL / 1-PALMITOYL-2-OLEOYL-SN-GLYCERO-3-[PHOSPHO-RAC-(1-GLYCEROL)](SODIUM SALT) / Phosphatidylglycerol Mass: 751.023 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄₀H₇₉O₁₀P / Comment: phospholipid*YM
#4: Chemical	ChemComp-CHT / CHOLINE ION / Choline Mass: 104.171 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₅H₁₄NO
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 32 / 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: 3.82 Å³/Da / Density % sol: 67.81 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop Details: PEG 400, NaCl, NaCitrate, Choline, VAPOR DIFFUSION, HANGING DROP, temperature 291K PH range: 5.3-5.6

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Data collection

Diffraction source

Source:

SYNCHROTRON / Site:

NSLS

/ Beamline: X29A / Wavelength: 1 Å

Detector

Type: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 17, 2010

Radiation

Monochromator: AL3 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 3.21→29.802 Å / Num. obs: 38765 / % possible obs: 82.6 % / Observed criterion σ(I): -3 / B_iso Wilson estimate: 89.291 Å² / R_merge(I) obs: 0.106 / Net I/σ(I): 14.77

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Highest resolution (Å)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. unique obs	% possible all
3.21-3.29		0.201	11.63	3249	258	7.5
3.29-3.38		0.234	9.23	9128	781	23.4
3.38-3.48		0.373	5.99	17453	1518	46.7
3.48-3.58		0.446	4.84	30856	2700	85.3
3.58-3.7		0.429	4.97	35638	3054	100
3.7-3.83		0.332	6.25	34733	2953	99.9
3.83-3.98		0.266	7.66	33974	2868	99.9
3.98-4.14		0.199	9.69	32447	2733	99.9
4.14-4.32		0.163	11.81	31539	2651	99.8
4.32-4.53		0.144	14.16	30244	2546	99.9
4.53-4.78		0.122	16.83	28494	2409	99.9
4.78-5.07		0.115	18.39	27325	2303	100
5.07-5.42		0.108	19.33	25575	2164	100
5.42-5.85		0.104	21.54	23695	2025	100
5.85-6.41		0.096	23.42	21534	1858	99.9
6.41-7.17		0.088	27.05	19244	1709	100
7.17-8.28		0.079	30.05	16297	1513	100
8.28-10.14		0.074	32.94	14345	1295	100
10.14-14.34		0.067	32.32	10658	1004	97.7
	14.34	0.066	28.93	3787	423	69.9

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

R_factor: 33.61 / Model details: Phaser MODE: MR_AUTO

	Highest resolution	Lowest resolution
Rotation	3.21 Å	29.8 Å
Translation	3.21 Å	29.8 Å

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Processing

Software

Name	Version	Classification
XSCALE		data scaling
PHASER	2.1.4	phasing
PHENIX	1.7_650	refinement
PDB_EXTRACT	3.1	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 3.25→29.802 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.45 / σ(F): 1.99 / Phase error: 30.39 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2969	3841	9.93 %
R_work	0.2494	-	-
obs	0.2542	38678	86 %

Solvent computation

Shrinkage radii: 0.38 Å / VDW probe radii: 0.7 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 88.989 Å² / k_sol: 0.295 e/Å³

Displacement parameters

B_iso max: 499.43 Å² / B_iso mean: 118.5717 Å² / B_iso min: 8.22 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.6595 Å²	0 Å²	-0 Å²
2-	-	1.9216 Å²	0 Å²
3-	-	-	-1.2622 Å²

Refinement step

Cycle: LAST / Resolution: 3.25→29.802 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11671	0	60	32	11763

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	12042
X-RAY DIFFRACTION	f_angle_d	0.704	16399
X-RAY DIFFRACTION	f_chiral_restr	0.048	1902
X-RAY DIFFRACTION	f_plane_restr	0.003	2017
X-RAY DIFFRACTION	f_dihedral_angle_d	13.889	4048

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 27

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
3.2501-3.2911	0.3549	10	0.3159	174	184	11
3.2911-3.3344	0.3773	25	0.2731	289	314	20
3.3344-3.38	0.3013	49	0.3147	415	464	28
3.38-3.4282	0.3395	59	0.3398	584	643	39
3.4282-3.4793	0.3456	82	0.3177	828	910	55
3.4793-3.5336	0.3576	126	0.3028	1153	1279	78
3.5336-3.5915	0.3578	158	0.2874	1396	1554	95
3.5915-3.6533	0.3549	165	0.2958	1491	1656	100
3.6533-3.7196	0.2897	164	0.2828	1473	1637	100
3.7196-3.791	0.316	167	0.258	1502	1669	100
3.791-3.8682	0.3363	162	0.2498	1455	1617	100
3.8682-3.9521	0.2866	166	0.2518	1496	1662	100
3.9521-4.0439	0.2812	165	0.2469	1492	1657	100
4.0439-4.1447	0.3002	164	0.2553	1467	1631	100
4.1447-4.2565	0.2766	167	0.2306	1505	1672	100
4.2565-4.3814	0.2908	164	0.2337	1480	1644	100
4.3814-4.5223	0.2875	167	0.2339	1505	1672	100
4.5223-4.6833	0.2765	165	0.2311	1481	1646	100
4.6833-4.8701	0.2718	168	0.2356	1517	1685	100
4.8701-5.0907	0.2855	167	0.2619	1495	1662	100
5.0907-5.3576	0.3727	167	0.2737	1510	1677	100
5.3576-5.6911	0.3405	166	0.2733	1491	1657	100
5.6911-6.127	0.3192	169	0.2624	1523	1692	100
6.127-6.7372	0.3239	169	0.2572	1516	1685	100
6.7372-7.6973	0.3115	170	0.2234	1540	1710	100
7.6973-9.643	0.1943	173	0.1708	1555	1728	100
9.643-29.8027	0.2934	167	0.265	1504	1671	92

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	0.1374	0.0222	0.0786	0.0107	0.0088	0.0389	-0.0362	0.2008	0.0399	-0.3495	0.0012	0.1592	-0.0478	-0.0967	-0.1469	0.588	0.0413	-0.6272	0.1269	-0.0274	0.1319	-17.422	-9.2198	13.1332
2	0.0597	-0.0242	0.0001	0.0078	-0.0017	0.0548	0.019	0.1544	-0.0114	-0.1399	-0.0851	0.0713	0.0063	-0.0736	-0.1313	0.9021	0.1112	-0.9179	0.3958	-0.187	0.5026	-17.5028	-12.8175	16.3873
3	0.1408	-0.1217	0.1071	0.3496	-0.0928	0.0781	0.0993	-0.1639	-0.0393	0.0063	-0.1139	-0.0076	-0.0146	-0.1195	-0.0071	0.8727	-0.0274	-0.4296	0.8714	-0.1213	1.0557	-37.7013	-20.8822	9.017
4	0.1772	0.0725	-0.0264	0.0282	-0.021	0.1465	-0.0148	0.3605	-0.1284	-0.4182	0.0611	0.284	0.196	-0.2236	0.014	0.9414	0.0613	-0.8384	0.4068	-0.168	0.531	-22.4023	-17.0707	16.939
5	0.0552	0.0071	-0.0167	0.0901	0.0013	0.122	-0.0353	-0.0688	0.0044	0.0804	-0.0257	0.0218	0.0348	0.0257	0.0127	0.6619	-0.018	-0.0479	0.4163	0.1788	0.3647	-0.0852	19.0534	55.9501
6	0.1729	-0.0405	0.0219	0.1936	0.0375	0.0373	-0.022	0.0573	0.1595	0.1482	-0.0112	-0.0638	-0.015	0.0202	-0.0777	0.0567	0.2244	0.123	0.5314	-0.1898	0.8337	-31.1046	-24.9617	59.2762
7	0.0535	-0.0018	-0.0835	0.0066	0.001	0.0643	0.0696	-0.0527	0.0866	0.1557	0.0723	0.1494	0.0115	-0.1523	0.1687	0.3308	0.1088	0.2579	0.0914	-0.1396	0.4623	-25.6591	-28.5465	58.8421
8	0.0257	0.0116	0.0191	0.0032	0.0072	0.0336	-0.0235	-0.0134	-0.0019	-0.0346	-0.0772	0.0586	-0.1208	-0.0848	-0.0083	1.102	-0.0501	0.5456	0.8763	-0.0358	0.8635	-24.5651	-34.7748	78.9085
9	0.0758	0.0958	0.0701	0.3666	-0.0137	0.2066	-0.1612	-0.3232	0.0898	0.4581	-0.0253	0.5771	-0.0529	-0.2951	-0.1921	0.3343	0.1593	0.4619	0.2214	-0.2981	0.1149	-20.7641	-31.0202	61.2268
10	0.0089	0.0064	-0.0053	0.006	-0.004	0.0029	-0.0111	-0.0024	0.0031	-0.0044	0.0223	-0.0101	-0.0132	0.037	-0.008	1.3015	0.2064	0.012	1.281	-0.0595	1.1047	-31.9429	6.4559	48.7604
11	0.1465	-0.0777	0.0082	0.069	-0.0699	0.1088	-0.0645	0.09	-0.0028	0.0756	-0.2204	-0.4145	0.0017	0.2866	-0.1848	0.0223	-0.0603	0.0246	0.4297	0.1236	0.3941	24.49	-22.8441	55.61
12	0.245	0.1252	0.0844	0.6598	-0.016	0.2321	-0.0719	-0.0742	-0.0314	-0.2033	-0.2831	-0.4088	0.1081	0.3032	-0.3078	0.3065	0.0184	0.1097	0.1151	0.0682	0.2618	8.9432	-10.9355	41.73
13	0.0149	0.0508	-0.0661	0.2088	-0.2204	0.3516	-0.1118	0.1875	-0.1037	-0.3656	-0.3991	-0.5826	0.0537	0.3147	-0.7081	0.1395	0.2473	0.4058	0.439	0.1843	0.5947	19.3569	-18.4776	38.6556
14	0.2333	-0.0291	0.1114	0.3256	-0.1114	0.1937	-0.0301	0.332	-0.2745	-0.4854	-0.157	-0.8852	0.2619	0.5071	-0.2767	-0.0842	-0.1087	0.33	0.2547	0.1083	0.6468	19.2453	-14.725	39.8761
15	0.0565	-0.0265	0.0052	0.0159	0.008	0.1196	-0.0482	0.0227	-0.0008	-0.0016	-0.1174	-0.1407	0.004	0.2073	0.0839	0.3466	-0.1461	0.1745	0.634	-0.0894	0.898	-15.3849	9.7465	57.8998
16	0.0321	-0.0156	0.0297	0.025	-0.0053	-0.0002	0.0092	-0.1351	-0.0177	-0.0223	0.0107	-0.0579	0.0699	0.029	0.0175	0.0615	0.1481	-0.0969	0.211	0.0908	0.209	-3.0741	-27.4507	44.1857
17	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1.3311	0.0356	-0.0594	1.3495	0.0723	1.3465	-17.7552	-35.1353	34.2713
18	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.7229	0.0366	0.0503	0.7116	-0.0019	0.7401	1.093	9.5561	49.3867
19	1.0637	-0.6162	-0.1309	1.092	0.9653	1.0908	-0.0287	0.0189	0.3658	-0.0217	-0.0343	-0.0249	-0.2786	0.0128	0.0277	0.5373	-0.1106	-0.1102	0.2471	-0.0483	0.3414	-9.0284	-2.9693	38.3912
20	6.998	7.0414	1.5318	7.2531	0.8897	2.863	0.1968	-2.9408	6.4941	2.284	-1.1469	1.401	-1.0074	-1.7645	0.9524	1.4233	0.1135	0.0096	1.4501	0.1278	1.089	18.6742	-11.8331	38.2868

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 57:154 )	A	57 - 154
2	X-RAY DIFFRACTION	2	( CHAIN A AND RESID 155:259 )	A	155 - 259
3	X-RAY DIFFRACTION	3	( CHAIN A AND RESID 260:325 )	A	260 - 325
4	X-RAY DIFFRACTION	4	( CHAIN A AND RESID 326:553 )	A	326 - 553
5	X-RAY DIFFRACTION	5	( CHAIN A AND RESID 554:583 )	A	554 - 583
6	X-RAY DIFFRACTION	6	( CHAIN B AND RESID 57:151 )	B	57 - 151
7	X-RAY DIFFRACTION	7	( CHAIN B AND RESID 152:271 )	B	152 - 271
8	X-RAY DIFFRACTION	8	( CHAIN B AND RESID 272:311 )	B	272 - 311
9	X-RAY DIFFRACTION	9	( CHAIN B AND RESID 312:546 )	B	312 - 546
10	X-RAY DIFFRACTION	10	( CHAIN B AND RESID 547:558 )	B	547 - 558
11	X-RAY DIFFRACTION	11	( CHAIN C AND RESID 57:109 )	C	57 - 109
12	X-RAY DIFFRACTION	12	( CHAIN C AND RESID 110:223 )	C	110 - 223
13	X-RAY DIFFRACTION	13	( CHAIN C AND RESID 224:373 )	C	224 - 373
14	X-RAY DIFFRACTION	14	( CHAIN C AND RESID 374:548 )	C	374 - 548
15	X-RAY DIFFRACTION	15	( CHAIN C AND RESID 549:568 )	C	549 - 568
16	X-RAY DIFFRACTION	16	( CHAIN A AND RESID 701:707 ) OR ( CHAIN C AND RESID 701:713 ) OR ( CHAIN B AND RESID 601:612 )	A	701 - 707
17	X-RAY DIFFRACTION	16	( CHAIN A AND RESID 701:707 ) OR ( CHAIN C AND RESID 701:713 ) OR ( CHAIN B AND RESID 601:612 )	C	701 - 713
18	X-RAY DIFFRACTION	16	( CHAIN A AND RESID 701:707 ) OR ( CHAIN C AND RESID 701:713 ) OR ( CHAIN B AND RESID 601:612 )	B	601 - 612
19	X-RAY DIFFRACTION	17	( CHAIN A AND RESID 601:601 )	A	601
20	X-RAY DIFFRACTION	18	( CHAIN C AND RESID 602:602 )	C	602
21	X-RAY DIFFRACTION	19	( CHAIN A AND RESID 602:602 )	A	602
22	X-RAY DIFFRACTION	20	( CHAIN C AND RESID 601:601 )	C	601

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