PDB-4llh: Substrate bound outward-open state of the symporter BetP

ID or keywords:

Entry

Database: PDB / ID: 4llh

Title

Substrate bound outward-open state of the symporter BetP

Components

Glycine betaine transporter BetP

Keywords

TRANSPORT PROTEIN / Secondary transporter

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 / Resolution: 2.8 Å

Authors

Perez, C. / Faust, B. / Ziegler, C.

Citation

Journal: Nat Commun / Year: 2014
Title: Substrate-bound outward-open state of the betaine transporter BetP provides insights into Na(+) coupling.
Authors: Perez, C. / Faust, B. / Mehdipour, A.R. / Francesconi, K.A. / Forrest, L.R. / Ziegler, C.

History

Deposition	Jul 9, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 7, 2014	Provider: repository / Type: Initial release
Revision 1.1	Jul 2, 2014	Group: Database references
Revision 1.2	Jul 30, 2014	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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _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	4llh.cif.gz	576.5 KB	Display	PDBx/mmCIF format
PDB format	pdb4llh.ent.gz	476.7 KB	Display	PDB format
PDBx/mmJSON format	4llh.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4llh_validation.pdf.gz	961.8 KB	Display	wwPDB validaton report
Full document	4llh_full_validation.pdf.gz	1 MB	Display
Data in XML	4llh_validation.xml.gz	62 KB	Display
Data in CIF	4llh_validation.cif.gz	83.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ll/4llh ftp://data.pdbj.org/pub/pdb/validation_reports/ll/4llh	HTTPS FTP

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Related structure data

Similar structure data	2wit-d 4doj-d 3p03-d 4ain-d 6zrx-d 5ngk-d 6jkp-d 21876 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)	115.470, 129.690, 164.650
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

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Protein , 1 types, 3 molecules ABC

#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) Strain: ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025 Gene: betP, Cgl0892, cg1016 / Plasmid: pASK-IBA7 / Production host: Escherichia coli (E. coli) / References: UniProt: P54582

#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)
Strain: ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025
Gene: betP, Cgl0892, cg1016 / Plasmid: pASK-IBA7 / Production host:

Escherichia coli (E. coli) / References: UniProt: P54582

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Non-polymers , 5 types, 99 molecules

#2: Chemical	ChemComp-1Y8 / 2-(trimethyl-lambda~5~-arsanyl)ethanol Mass: 165.086 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₅H₁₄AsO
#3: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical	ChemComp-CM5 / 5-CYCLOHEXYL-1-PENTYL-BETA-D-MALTOSIDE / 5-CYCLOHEXYLPENTYL 4-O-ALPHA-D-GLUCOPYRANOSYL-BETA-D-GLUCOPYRANOSIDE / CYMAL-5 Mass: 494.573 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₃H₄₂O₁₁ / Comment: detergent*YM
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 91 / 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: 3.36 Å³/Da / Density % sol: 63.34 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 100 mM Na3citrate, 300 mM NaCl, 17-24% PEG400, 8 mM arseno-choline, VAPOR DIFFUSION, HANGING DROP, temperature 298K PH range: 5.3-5.6

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Data collection

Diffraction source

Source:

SYNCHROTRON / Site:

SLS

/ Beamline: X10SA / Wavelength: 1.043

Detector

Type: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 17, 2012

Radiation

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

Radiation wavelength

Wavelength: 1.043 Å / Relative weight: 1

Reflection

Resolution: 2.8→36.33 Å / Num. obs: 48865 / R_merge(I) obs: 0.159 / Net I/σ(I): 12.47

Reflection shell

Resolution (Å)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique all	Diffraction-ID
2.8-3.04	0.301	5.4	380	1
3.04-3.78	0.622	3.88	3057	1
3.78-5.12	0.202	9.9	3310	1
5.12-6.27	0.059	19.9	2431	1
6.27-8.87	0.04	24.52	1990	1
8.87-12.5	0.018	37.32	1315	1

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Processing

Software

Name	Version	Classification
PHASER		phasing
PHENIX	(phenix.refine: 1.7_650)	refinement
XDS		data reduction
XDS		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.8→36.3 Å / SU ML: 0.43 / σ(F): 1.99 / Phase error: 30.93 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2896	2312	5.06 %
R_work	0.2405	-	-
obs	0.243	45722	82.46 %

Solvent computation

Shrinkage radii: 0.49 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 24.294 Å² / k_sol: 0.27 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.3865 Å²	-0 Å²	-0 Å²
2-	-	-4.6489 Å²	0 Å²
3-	-	-	-3.0734 Å²

Refinement step

Cycle: LAST / Resolution: 2.8→36.3 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11406	0	92	91	11589

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	11791
X-RAY DIFFRACTION	f_angle_d	0.74	16076
X-RAY DIFFRACTION	f_dihedral_angle_d	14.781	3890
X-RAY DIFFRACTION	f_chiral_restr	0.053	1886
X-RAY DIFFRACTION	f_plane_restr	0.002	1961

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 (%)
2.8-2.9593	0.4124	53	0.3552	996	X-RAY DIFFRACTION	32
2.9593-3.0236	0.4349	78	0.3188	1271	X-RAY DIFFRACTION	42
3.0236-3.0939	0.2938	59	0.3031	1573	X-RAY DIFFRACTION	51
3.0939-3.1713	0.3426	88	0.2815	1816	X-RAY DIFFRACTION	59
3.1713-3.2569	0.3395	118	0.2855	2015	X-RAY DIFFRACTION	67
3.2569-3.3527	0.3592	114	0.2859	2325	X-RAY DIFFRACTION	75
3.3527-3.4609	0.3699	127	0.2764	2574	X-RAY DIFFRACTION	84
3.4609-3.5844	0.3186	167	0.2535	2828	X-RAY DIFFRACTION	92
3.5844-3.7278	0.3136	170	0.2413	3037	X-RAY DIFFRACTION	99
3.7278-3.8973	0.2949	191	0.2255	3012	X-RAY DIFFRACTION	99
3.8973-4.1025	0.263	159	0.2114	3099	X-RAY DIFFRACTION	100
4.1025-4.3591	0.2572	164	0.2077	3086	X-RAY DIFFRACTION	100
4.3591-4.6951	0.2528	166	0.2022	3082	X-RAY DIFFRACTION	100
4.6951-5.1664	0.2621	158	0.1993	3116	X-RAY DIFFRACTION	100
5.1664-5.9112	0.2567	156	0.2323	3142	X-RAY DIFFRACTION	100
5.9112-7.4369	0.2734	168	0.2508	3164	X-RAY DIFFRACTION	100
7.4369-36.333	0.2865	176	0.2631	3274	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	0.1262	-0.0347	-0.096	0.0381	0.0556	0.0923	-0.0101	0.1272	-0.0502	-0.2562	-0.0445	-0.1595	0.0992	0.0306	-0.0095	0.4695	0.0101	0.2948	0.2097	-0.0381	0.1787	11.7813	8.4985	5.9786
2	0.0175	-0.0319	-0.0323	0.1149	0.0633	0.083	-0.0726	0.0758	0.021	-0.1362	-0.0548	-0.0918	0.0436	0.048	-0.2549	0.6401	-0.0351	0.4006	0.1207	0.0973	0.1941	12.2275	12.2187	8.8494
3	0.0377	0.0088	-0.0378	0.0007	-0.0003	0.0384	0.008	-0.0202	-0.0248	-0.0351	-0.0004	0.008	-0.0182	0.0386	0.0178	0.4406	-0.0407	0.4309	0.1457	0.048	0.2846	30.7415	19.315	-0.6419
4	0.0062	0.0945	-0.0349	0.2726	-0.0599	0.1492	0.0394	0.2844	-0.0843	-0.5418	-0.0214	-0.396	0.0746	0.2239	0.0755	0.32	-0.0519	0.8491	-0.0202	0.1446	-0.4926	17.0838	16.2779	8.6081
5	0.1936	-0.0339	-0.0405	0.7216	0.0269	0.0129	-0.0144	0.0012	-0.0336	0.2752	-0.0408	0.0492	0.0319	0.0021	0.0294	0.3899	-0.1005	-0.0831	0.2189	-0.0255	0.3462	2.3694	-20.0476	50.899
6	0.1455	-0.0119	-0.0813	-0.0006	0.0043	0.0531	-0.0622	-0.0178	-0.032	0.1216	-0.0711	-0.1233	-0.0158	0.0877	-0.0997	0.1824	0.2752	-0.2274	0.2353	0.0164	0.4318	33.0519	24.695	48.7971
7	0.1314	0.0266	0.048	0.0182	-0.0251	0.0827	-0.0114	-0.0147	-0.0032	0.1435	-0.0919	-0.2638	0.0597	0.2379	0.048	0.1028	0.219	-0.205	0.2702	0.0564	0.3081	27.5225	28.5915	49.2209
8	0.0142	-0.0082	0.0136	0.0154	-0.0194	0.0193	-0.0016	-0.0263	-0.007	0.0218	-0.0086	-0.0313	0.0495	0.054	-0.0111	0.6706	0.1149	-0.3811	0.4672	0.0131	0.4024	29.4603	34.1419	68.5474
9	0.0242	0.0234	-0.0161	0.5072	0.0236	0.1775	-0.087	-0.2546	0.0305	0.519	-0.0145	-0.5579	-0.0163	0.2414	-0.0442	0.227	0.146	-0.4243	0.1644	0.1992	0.0094	22.8597	30.7736	52.4092
10	3.3363	2.8077	-1.0131	2.9278	-0.7537	1.9743	-0.0456	0.121	0.5479	0.2029	-0.01	0.008	-0.3713	0.0002	0.0561	0.7451	0.0433	-0.0051	0.6103	0.0536	0.7001	31.7344	-2.0046	46.1023
11	0.0109	-0.0007	-0.01	-0.0009	0.0039	0.0127	0.0084	-0.0225	-0.01	0.0765	-0.0067	0.1071	0.0261	-0.0083	-0.0154	0.1551	0.0701	0.2065	0.176	-0.0098	0.1653	-22.3992	21.8037	53.8767
12	0.1372	0.0472	-0.0087	0.0761	0.0473	0.1205	-0.0392	-0.1643	-0.0319	-0.0117	-0.0655	0.0279	-0.0134	0.0083	-0.2632	-0.0726	0.0589	-0.1374	-0.0745	0.1398	-0.2747	-9.3191	10.167	38.1807
13	0.0755	0.1134	0.0114	0.2678	0.0275	0.0945	-0.0037	-0.1983	0.0632	0.0289	-0.0593	0.4189	-0.0524	-0.0819	-0.058	0.0213	0.0761	0.0116	0.346	-0.0132	0.2851	-19.9822	17.4748	36.927
14	0.2653	0.0365	0.1783	0.5257	0.1012	0.4473	-0.1011	0.0213	0.2174	-0.1696	-0.1023	0.5836	-0.1647	-0.4662	-0.2886	-0.0418	0.028	-0.1354	0.1911	-0.0235	0.2537	-19.9106	13.7208	37.9476
15	0.2237	0.445	0.2018	0.8856	0.4018	0.1823	-0.044	0.0383	-0.0593	-0.0447	0.1135	-0.2178	-0.0015	0.0888	-0.0788	0.6802	0.0026	0.0257	0.7887	-0.1059	0.7851	7.355	-7.5382	49.8066
16	2.2785	0.9574	-0.4587	1.9815	1.7721	2.5372	1.1265	1.0246	0.8876	1.6557	-0.7164	-0.4701	-4.213	-0.5396	-0.4101	1.0432	0.0259	-0.0157	0.842	0.1279	1.2697	26.2415	31.7852	51.4382
17	2	4.2767	3.9381	2	0.3969	2	0.8307	0.0635	-5.1499	0.0327	-0.5538	-3.0631	1.5399	-1.6187	-0.2793	0.7244	0.2233	-0.0331	0.4603	-0.0574	0.7993	16.4567	17.3597	5.448
18	0.0141	0.0002	0.0015	0.0256	-0.0071	-0.0026	-0.0166	-0.0218	0.0185	-0.024	0.0028	-0.0449	0.0066	0.0088	0.0117	-0.1426	0.0432	0.0711	0.0716	0.0276	-0.0161	4.5753	24.7715	32.6858
19	0	0	0	0	-0	-0	0	0	0	-0	0	0	-0	0	-0	0.4679	0.09	-0.0618	0.4461	0.0354	0.5004	-0.113	-10.1227	44.6843
20	0.0095	-0.0193	0.005	0.048	-0.0154	0.0059	-0.0014	0.0303	-0.0321	0.0349	0.026	-0.0403	0.0108	0.0113	-0.0159	0.7233	0.1571	-0.0476	0.3985	-0.0359	0.5133	0.6244	-5.2292	34.1665
21	0.4923	-0.5886	-0.1803	0.7448	0.4514	1.4242	-1.0311	0.4208	-1.2257	-1.8742	0.8226	0.5557	0.6184	0.3045	0.2115	0.6877	0.0644	-0.0129	0.6188	0.1135	0.6952	-18.8034	11.688	36.8598
22	0.0048	0.0131	0.0039	0.036	0.0104	0.0029	0.0071	-0.0011	0.0229	-0.0214	-0.0153	0.042	-0.0196	-0.0198	0.0127	1.2686	0.0718	-0.0235	1.1662	-0.0452	1.1821	-13.7519	16.834	7.4913
23	0	-0	-0	0	0	0	-0.0008	-574465.7465	3259160.2261	574465.7475	0.0003	1965136.1509	-3259160.226	-1965136.1525	0.0005	2.344	-0.0125	-0.0032	2.3443	-0.0036	2.3461	23.2295	29.1435	60.4842
24	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.7964	-0.0261	0.0013	0.7911	0.0178	0.8028	23.4675	14.8126	4.2184

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 547:548 )	B	547 - 548
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 549:553 )	C	549 - 553
16	X-RAY DIFFRACTION	16	( CHAIN B AND RESID 601:601 )	B	601
17	X-RAY DIFFRACTION	17	( CHAIN A AND RESID 601:601 )	A	601
18	X-RAY DIFFRACTION	18	( CHAIN A AND RESID 701:725 ) OR ( CHAIN C AND RESID 701:740 ) OR ( CHAIN B AND RESID 701:726 )	A	701 - 725
19	X-RAY DIFFRACTION	18	( CHAIN A AND RESID 701:725 ) OR ( CHAIN C AND RESID 701:740 ) OR ( CHAIN B AND RESID 701:726 )	C	701 - 740
20	X-RAY DIFFRACTION	18	( CHAIN A AND RESID 701:725 ) OR ( CHAIN C AND RESID 701:740 ) OR ( CHAIN B AND RESID 701:726 )	B	701 - 726
21	X-RAY DIFFRACTION	19	( CHAIN C AND RESID 601:601 )	C	601
22	X-RAY DIFFRACTION	20	( CHAIN C AND RESID 602:602 )	C	602
23	X-RAY DIFFRACTION	21	( CHAIN C AND RESID 603:603 )	C	603
24	X-RAY DIFFRACTION	22	( CHAIN C AND RESID 604:604 )	C	604
25	X-RAY DIFFRACTION	23	( CHAIN B AND RESID 602:602 )	B	602
26	X-RAY DIFFRACTION	24	( CHAIN A AND RESID 602:602 )	A	602

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