PDB-3p03: Crystal structure of BetP-G153D with choline bound

ID or keywords:

Entry

Database: PDB / ID: 3p03

Title

Crystal structure of BetP-G153D with choline bound

Components

Glycine betaine transporter BetP

Keywords

TRANSPORT PROTEIN / Secondary transporter

Function / homology

Function and homology information

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: 3.35 Å

Authors

Perez, C. / Ressl, S. / Ziegler, Z.

Citation

Journal: Embo J. / Year: 2011
Title: Substrate specificity and ion coupling in the Na(+)/betaine symporter BetP.
Authors: Perez, C. / Koshy, C. / Ressl, S. / Nicklisch, S. / Kramer, R. / Ziegler, C.

History

Deposition	Sep 27, 2010	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 30, 2011	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Feb 21, 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	3p03.cif.gz	585.4 KB	Display	PDBx/mmCIF format
PDB format	pdb3p03.ent.gz	488 KB	Display	PDB format
PDBx/mmJSON format	3p03.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3p03_validation.pdf.gz	475.1 KB	Display	wwPDB validaton report
Full document	3p03_full_validation.pdf.gz	610.1 KB	Display
Data in XML	3p03_validation.xml.gz	72.4 KB	Display
Data in CIF	3p03_validation.cif.gz	94.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/p0/3p03 ftp://data.pdbj.org/pub/pdb/validation_reports/p0/3p03	HTTPS FTP

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Related structure data

Similar structure data	4ain-d 2wit-d 4llh-d 1up7-1 4c7r-d 5eft-d 1up6-2 0707 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

183 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)	117.560, 129.310, 183.140
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: 61060.508 Da / Num. of mol.: 3 / Fragment: UNP residues 30-595 / Mutation: E44A, E45A, E46A, 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-CHT / CHOLINE ION Mass: 104.171 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₅H₁₄NO

#1: Protein

Glycine betaine transporter BetP

Mass: 61060.508 Da / Num. of mol.: 3 / Fragment: UNP residues 30-595 / Mutation: E44A, E45A, E46A, 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-CHT / CHOLINE ION

Mass: 104.171 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₅H₁₄NO

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 3.8 Å³/Da / Density % sol: 67.63 %
Crystal grow	Temperature: 291 K / Method: hanging drop / pH: 5.5 Details: 22% PEG 400, 100 mM NaCl, 100 mM Na3Citrate, 5 mM Choline, pH 5.5, hanging drop, temperature 291K

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Data collection

Diffraction

Mean temperature: 298 K

Diffraction source

Source:

SYNCHROTRON / Site:

ESRF

/ Beamline: ID29 / Wavelength: 1 Å

Detector

Type: MAR CCD 165 mm / Detector: CCD / Date: Jun 19, 2009

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: 3.3→46.2 Å / Num. obs: 42602 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / B_iso Wilson estimate: 101.254 Å² / R_merge(I) obs: 0.127 / Net I/σ(I): 14.54

Reflection shell

Resolution (Å)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. unique obs	% possible all
3.3-3.5	0.717	3.1	78410	6812	100
3.5-3.8	0.453	5.2	96411	7722	100
3.8-4.5	0.25	10.9	173894	11007	99.9
4.5-6	0.131	20.4	154194	9750	100
6-8	0.093	30	63423	4193	100
8-10	0.075	37.7	22257	1517	100
10-15	0.068	37.4	16132	1158	100
15-35	0.058	31.2	4481	433	90.2
35-46	0.05	17.8	39	10	20.4

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

R_factor: 46.05 / Model details: Phaser MODE: MR_AUTO

	Highest resolution	Lowest resolution
Rotation	3.48 Å	34.75 Å
Translation	3.48 Å	34.75 Å

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Processing

Software

Name	Version	Classification
XSCALE		data scaling
PHASER	2.1.4	phasing
PHENIX	1.6.2_432	refinement
PDB_EXTRACT	3.1	data extraction
XDS		data scaling
XDS		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 3.35→46.2 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7817 / SU ML: 0.43 / σ(F): 1.99 / Phase error: 28.58 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.3004	3705	9.95 %
R_work	0.2446	33514	-
obs	0.2502	37219	91.18 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 74.407 Å² / k_sol: 0.273 e/Å³

Displacement parameters

B_iso max: 560.78 Å² / B_iso mean: 107.8704 Å² / B_iso min: 3.18 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.196 Å²	0 Å²	-0 Å²
2-	-	3.8118 Å²	-0 Å²
3-	-	-	-3.6158 Å²

Refinement step

Cycle: LAST / Resolution: 3.35→46.2 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11342	0	7	0	11349

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	11771
X-RAY DIFFRACTION	f_angle_d	1.11	16034
X-RAY DIFFRACTION	f_chiral_restr	0.069	1865
X-RAY DIFFRACTION	f_plane_restr	0.004	1972
X-RAY DIFFRACTION	f_dihedral_angle_d	18.157	3890

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
3.35-3.4697	0.3109	117	0.2819	1053	1170	29
3.4697-3.6086	0.343	317	0.2529	3014	3331	83
3.6086-3.7728	0.2944	396	0.2391	3638	4034	100
3.7728-3.9716	0.2797	397	0.2232	3646	4043	100
3.9716-4.2202	0.2875	388	0.214	3656	4044	100
4.2202-4.5458	0.2901	408	0.225	3631	4039	100
4.5458-5.0028	0.2856	407	0.2321	3671	4078	100
5.0028-5.7256	0.3244	433	0.2545	3670	4103	100
5.7256-7.2092	0.3284	393	0.2628	3750	4143	100
7.2092-46.2	0.27	449	0.2426	3785	4234	98

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	0.5838	-0.1415	-0.2393	0.6325	-0.1084	0.1379	0.1925	-0.2666	0.0448	1.0093	-0.0111	0.6322	-0.2008	-0.057	0.2008	1.1016	0.1094	0.724	0.2771	-0.0475	0.4422	-17.7513	9.0029	77.9343
2	0.3757	0.2007	0.1332	0.2087	0.1886	0.2497	0.2726	-0.3736	0.2916	0.2795	-0.4636	0.1757	0.2405	0.0155	-0.1546	1.3269	-0.2079	0.897	0.2978	-0.178	0.5761	-17.3895	12.8293	75.3136
3	0.2179	-0.0376	-0.147	0.076	0.0826	0.134	0.241	0.108	0.0561	0.093	-0.225	0.1879	-0.1561	-0.2804	0.1183	0.3156	-0.0288	0.47	0.8136	-0.2624	1.1211	-37.3861	20.4962	81.7728
4	0.9351	-0.0874	-0.0641	1.3717	-0.6515	0.4084	-0.2325	-0.7132	0.1302	1.3505	0.0126	0.7513	-0.0754	-0.0575	-0.3801	1.0698	-0.1763	0.8587	0.385	-0.0794	0.5552	-22.3037	16.6527	73.2269
5	0.8805	-0.0487	0.2768	0.3779	0.3316	0.6283	0.0811	0.218	-0.2142	-0.531	-0.0503	0.2386	-0.2945	0.3229	-0.0227	0.803	-0.0615	0.0611	0.1822	0.1041	0.2618	-0.1814	-19.0281	36.0895
6	0.3694	-0.2838	0.1297	0.4668	-0.2083	0.3449	0.0102	-0.0536	-0.278	-0.3584	0.0884	0.4241	0.2939	-0.2419	-0.0821	0.1493	-0.3574	-0.145	0.4269	-0.1534	0.9055	-30.4974	24.2203	32.6736
7	0.5447	0.0988	0.7988	1.7005	0.1352	1.1657	0.174	-0.1806	-0.0855	-0.6757	-0.182	1.0816	-0.0131	-0.6279	0.1876	0.3003	-0.0193	-0.3409	0.3089	-0.1439	0.7983	-25.6214	28.4918	33.4725
8	0.0742	-0.1194	-0.2439	0.1794	0.3823	0.7866	0.094	0.2353	-0.1689	0.0909	-0.1665	0.0915	0.469	-0.3014	0.0692	0.5602	-0.1068	-0.569	0.8314	0.1778	0.6892	-24.3211	31.9511	12.5273
9	0.3604	-0.3143	0.3212	0.8962	0.2567	0.6495	-0.0954	0.159	-0.1916	-0.5279	-0.2182	0.797	-0.1121	-0.2407	0.1529	0.4326	0.0601	-0.2928	0.3214	-0.2755	0.5364	-20.6418	31.0734	30.9425
10	0.136	0.0717	0.0272	0.1226	0.0199	0.0056	-0.008	-0.0332	-0.0679	-0.0307	0.1738	0.0163	0.0108	0.0196	-0.0724	1.1359	-0.6506	-0.2094	1.6693	0.2693	0.8	-31.9943	-6.5264	43.379
11	0.0341	-0.0508	0.2191	6.6397	-2.6841	2.7067	0.182	-0.0514	0.2143	-0.4046	-0.9662	-1.7455	0.0428	0.9214	0.2833	-0.0045	-0.0027	-0.0355	0.3055	-0.0203	0.4808	24.3617	22.7906	36.3407
12	0.5687	0.2436	0.5142	2.624	-0.1465	1.2246	0.0909	0.1651	-0.1112	0.4822	-0.3144	-0.8849	0.0242	0.4122	0.2537	0.1871	-0.0313	-0.0704	0.1445	0.1181	0.2477	8.9647	10.906	50.2034
13	0.1071	-0.2179	0.2378	2.4655	-1.1344	1.392	-0.2793	0.0319	0.3	0.8144	-0.5217	-1.3774	-0.2109	0.588	0.0661	0.209	-0.1729	-0.3426	0.3963	0.145	0.756	19.2143	18.2274	53.1869
14	0.1616	-0.0036	-0.1779	3.264	-0.2797	0.4139	0.2807	-0.0694	0.0743	0.7985	-0.3417	-1.6768	0.0144	0.4428	0.2366	-0.0684	0.0764	-0.3069	0.1814	0.2124	0.8035	19.247	14.6999	51.9716
15	0.0459	0.0194	0.1547	1.4147	-0.552	0.7863	-0.1781	-0.0699	0.0861	0.0121	-0.2487	0.0349	-0.2784	-0.2204	0.3744	0.2463	0.3766	-0.3789	0.8019	-0.4385	0.7885	-15.3734	-9.7256	34.1159

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 554:589)	A	554 - 589
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

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