PDB-6fxg: Crystal structure of substrate binding domain 1 (SBD1) OF ABC tra...

ID or keywords:

Entry

Database: PDB / ID: 6fxg

Title

Crystal structure of substrate binding domain 1 (SBD1) OF ABC transporter GLNPQ in complex with Asparagine

Components

Amino acid ABC transporter membrane protein PAAT family

Keywords

TRANSPORT PROTEIN / ASPARAGINE BINDING PROTEIN / AMINO ACID TRANSPORT / EXTRACELLULAR

Function / homology

Function and homology information

peptide transport / ligand-gated monoatomic ion channel activity / ATP-binding cassette (ABC) transporter complex / protein transport
Similarity search - Function

Biological species

Lactococcus lactis subsp. lactis (lactic acid bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.7 Å

Authors

Guskov, A. / Schuurman-Wolters, G.K. / Poolman, B.

Funding support

Netherlands, 1items

Citation

Journal: To Be Published
Title: Crystal structure of substrate binding domain 1 (SBD1) OF ABC transporter GLNPQ in complex with Asparagine
Authors: Schuurman-Wolters, G.K. / Guskov, A. / Poolman, B.

History

Deposition	Mar 9, 2018	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Mar 20, 2019	Provider: repository / Type: Initial release
Revision 1.1	Jan 17, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6fxg.cif.gz	291 KB	Display	PDBx/mmCIF format
PDB format	pdb6fxg.ent.gz	239.2 KB	Display	PDB format
PDBx/mmJSON format	6fxg.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6fxg_validation.pdf.gz	436.5 KB	Display	wwPDB validaton report
Full document	6fxg_full_validation.pdf.gz	437.4 KB	Display
Data in XML	6fxg_validation.xml.gz	34.8 KB	Display
Data in CIF	6fxg_validation.cif.gz	54.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fx/6fxg ftp://data.pdbj.org/pub/pdb/validation_reports/fx/6fxg	HTTPS FTP

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Related structure data

Related structure data	4kptS S: Starting model for refinement
Similar structure data	4zv2-d 1wdn-d 3frw-4 4dfd-2 5a76-3 5nh1-d 4ymx-2 4f72-2 1i7a-8 6mlo-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) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

4kptS

S: Starting model for refinement

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#235 - Jul 2019 AMPA Receptor similarity (2)

Deposited unit

A: Amino acid ABC transporter membrane protein PAAT family

B: Amino acid ABC transporter membrane protein PAAT family

C: Amino acid ABC transporter membrane protein PAAT family

hetero molecules

74.5 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Amino acid ABC transporter membrane protein PAAT family

hetero molecules

defined by author
Evidence: light scattering
24.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Amino acid ABC transporter membrane protein PAAT family

hetero molecules

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

3

C: Amino acid ABC transporter membrane protein PAAT family

hetero molecules

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

Unit cell

Length a, b, c (Å)	41.870, 74.270, 110.240
Angle α, β, γ (deg.)	90.00, 90.55, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Amino acid ABC transporter membrane protein PAAT family Mass: 24707.889 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Details: GM are cloning artefacts, the real sequence starts from E, which should be # 27 Source: (gene. exp.) Lactococcus lactis subsp. lactis (lactic acid bacteria) Gene: LL275_1813 / Production host: Lactococcus lactis (lactic acid bacteria) / References: UniProt: A0A1V0NHP2, UniProt: Q9CES5*PLUS
#2: Chemical	ChemComp-ASN / ASPARAGINE Type: L-peptide linking / Mass: 132.118 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₄H₈N₂O₃
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 941 / 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: 2.3 Å³/Da / Density % sol: 46.55 %
Crystal grow	Temperature: 273 K / Method: microbatch / pH: 4.5 Details: 0.1M CH3COONa pH4.5, 0.05 M (CH3COO)Ca2, 40 % v/v propanediol

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 31, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.7→44.261 Å / Num. obs: 135138 / % possible obs: 92.5 % / Redundancy: 1.84 % / R_rim(I) all: 0.04 / Net I/σ(I): 15.2
Reflection shell	Resolution: 1.7→1.72 Å / R_rim(I) all: 0.101 / % possible all: 74

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Processing

Software

Name	Version	Classification
PHENIX	(1.12_2829: ???)	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4KPT

4kpt

Resolution: 1.7→44.26 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.14 / Phase error: 16.99

	R_factor	Num. reflection	% reflection
R_free	0.17	6742	4.99 %
R_work	0.136	-	-
obs	0.138	135138	92.5 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 1.7→44.26 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5168	0	25	941	6134

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	5415
X-RAY DIFFRACTION	f_angle_d	0.981	7323
X-RAY DIFFRACTION	f_dihedral_angle_d	12.159	3245
X-RAY DIFFRACTION	f_chiral_restr	0.056	789
X-RAY DIFFRACTION	f_plane_restr	0.007	954

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 (%)
1.7-1.7193	0.2185	174	0.1896	3416	X-RAY DIFFRACTION	74
1.7193-1.7396	0.2281	199	0.1827	3767	X-RAY DIFFRACTION	81
1.7396-1.7608	0.2342	209	0.1801	4075	X-RAY DIFFRACTION	89
1.7608-1.7831	0.2107	228	0.1745	4249	X-RAY DIFFRACTION	92
1.7831-1.8065	0.2281	238	0.1748	4496	X-RAY DIFFRACTION	95
1.8065-1.8313	0.2132	223	0.1691	4393	X-RAY DIFFRACTION	96
1.8313-1.8575	0.1979	233	0.1649	4390	X-RAY DIFFRACTION	95
1.8575-1.8852	0.1911	229	0.1567	4377	X-RAY DIFFRACTION	95
1.8852-1.9146	0.1909	228	0.1496	4368	X-RAY DIFFRACTION	95
1.9146-1.946	0.2027	230	0.1606	4347	X-RAY DIFFRACTION	95
1.946-1.9796	0.2009	233	0.1604	4395	X-RAY DIFFRACTION	94
1.9796-2.0156	0.1921	223	0.1545	4309	X-RAY DIFFRACTION	94
2.0156-2.0544	0.1674	227	0.1434	4323	X-RAY DIFFRACTION	93
2.0544-2.0963	0.1679	223	0.1416	4299	X-RAY DIFFRACTION	92
2.0963-2.1419	0.1856	223	0.1401	4167	X-RAY DIFFRACTION	90
2.1419-2.1917	0.1855	227	0.1421	4360	X-RAY DIFFRACTION	93
2.1917-2.2465	0.1762	233	0.1338	4364	X-RAY DIFFRACTION	95
2.2465-2.3072	0.1829	230	0.1375	4390	X-RAY DIFFRACTION	95
2.3072-2.3751	0.158	231	0.1226	4366	X-RAY DIFFRACTION	95
2.3751-2.4518	0.1491	228	0.1236	4452	X-RAY DIFFRACTION	95
2.4518-2.5394	0.1604	228	0.1214	4300	X-RAY DIFFRACTION	94
2.5394-2.6411	0.1707	224	0.1259	4363	X-RAY DIFFRACTION	94
2.6411-2.7612	0.1694	228	0.1284	4310	X-RAY DIFFRACTION	93
2.7612-2.9068	0.1662	225	0.134	4230	X-RAY DIFFRACTION	92
2.9068-3.0889	0.1782	217	0.1421	4159	X-RAY DIFFRACTION	90
3.0889-3.3273	0.1679	234	0.1327	4336	X-RAY DIFFRACTION	94
3.3273-3.662	0.1458	232	0.1263	4351	X-RAY DIFFRACTION	94
3.662-4.1915	0.154	230	0.1147	4387	X-RAY DIFFRACTION	94
4.1915-5.2795	0.1489	229	0.1065	4330	X-RAY DIFFRACTION	93
5.2795-44.2758	0.1461	226	0.1472	4327	X-RAY DIFFRACTION	94

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	2.4959	-2.2171	0.3151	5.9225	0.2188	2.06	0.0148	-0.0354	0.0701	0.1495	0.0665	-0.0866	0.0137	-0.2008	-0.0457	0.0642	-0.0099	0.0344	0.1428	0.0255	0.0592	37.6019	12.3981	147.3649
2	7.3698	5.8155	6.9901	4.5902	5.5067	7.0331	0.1282	-0.1717	-0.0512	0.2826	-0.0674	-0.0303	0.1212	-0.1194	0.0146	0.1593	-0.002	-0.0163	0.1289	0.0152	0.108	48.5668	6.0975	155.9388
3	1.9979	2.0366	-1.979	3.1674	-4.4702	7.474	-0.0007	-0.1132	0.1063	0.3944	-0.02	-0.1671	-0.2099	0.0369	0.0565	0.148	-0.0118	-0.0402	0.0974	-0.0175	0.1293	55.8759	19.7389	152.5388
4	5.7308	-0.8623	-1.8246	5.3633	1.8833	3.8041	0.2141	0.0308	0.441	-0.0927	-0.0037	-0.1587	-0.3198	-0.165	-0.0565	0.19	-0.0328	0.025	0.0978	0.0017	0.0763	48.0542	54.805	156.9291
5	2.9578	-1.2744	0.3458	2.1065	0.8231	3.2538	0.072	0.0342	0.2636	0.0036	0.0358	-0.2086	-0.2513	0.0431	-0.0389	0.2144	-0.0208	0.0606	0.0721	-0.0115	0.1571	47.8003	56.051	155.9468
6	0.6572	-0.4157	0.1232	1.0026	-0.0327	0.8145	0.0217	-0.0211	-0.0329	0.117	-0.0099	-0.0272	0.0052	-0.0338	-0.0166	0.168	-0.0375	0.0108	0.1139	-0.0115	0.1274	51.7464	40.0397	157.7498
7	7.1112	0.0931	-1.4107	5.1564	-0.6978	5.2346	0.0009	-0.0869	-0.3232	-0.0757	-0.0054	-0.3032	0.1229	0.3942	0.1126	0.1504	0.0226	-0.0247	0.1444	-0.0354	0.0881	44.2807	60.4715	117.4331
8	3.8986	1.238	-0.2147	3.9989	-0.7138	4.2245	-0.1217	0.1346	-0.4135	-0.1406	0.1604	-0.2562	0.3572	0.3616	0.051	0.1783	0.0126	0.0007	0.1597	-0.0617	0.1621	43.8413	56.1039	111.2161
9	0.973	0.7839	-0.3473	2.1215	-0.4062	3.7175	-0.0828	0.0943	-0.0739	-0.0905	0.1577	-0.143	0.0657	0.5253	-0.0945	0.1043	-0.019	-0.0131	0.2113	-0.0328	0.1303	48.4993	66.0863	119.2215
10	0.9741	0.207	-0.5013	1.344	0.3515	2.3847	-0.026	-0.0306	0.0028	-0.031	-0.0674	0.2019	0.0564	-0.2179	0.0418	0.1009	-0.0112	-0.0272	0.1462	-0.0177	0.1361	29.8157	66.0087	130.9146
11	2.1803	1.1154	-1.3539	1.745	-0.6171	2.8678	-0.1105	0.0703	-0.0382	-0.1149	0.0224	0.0914	0.1002	-0.2737	0.0867	0.157	-0.0169	-0.0349	0.1426	-0.0217	0.124	30.6682	62.4853	122.6983
12	4.9047	3.7176	5.9389	3.7871	5.0599	7.5769	-0.2264	0.2162	0.2549	-0.1286	0.146	0.0278	-0.4946	0.3296	0.0491	0.316	-0.0542	-0.0015	0.1858	-0.0002	0.1224	40.2875	68.5647	103.3736
13	5.2237	2.3372	-2.9313	6.9199	-4.3047	3.5192	0.0207	0.1717	0.0164	0.0323	0.2115	0.48	0.7009	-0.649	-0.1248	0.2765	-0.0687	-0.0132	0.1997	-0.0189	0.1614	32.2562	55.5107	107.1958
14	0.3376	-0.1242	0.495	0.085	-0.1729	0.7183	-0.0251	-0.0206	-0.0116	0.1513	-0.0182	-0.1096	-0.0905	-0.017	0.042	0.0574	-0.012	0.03	0.1405	0.0042	0.094	42.1643	41.921	141.5743
15	1.8813	-1.8597	0.6821	2.6973	-1.2025	1.0853	0.097	0.0254	-0.175	-0.1711	0.053	0.072	0.1861	0.0223	-0.1269	0.1046	-0.0051	-0.0097	0.1056	-0.0024	0.0979	49.3682	10.0729	139.7322
16	1.7097	2.8233	-2.0154	5.8781	-3.5931	3.7815	-0.0729	0.0652	-0.1709	0.0435	-0.1278	-0.3915	0.136	0.1621	0.2685	0.0814	0.0091	-0.0239	0.1366	-0.0098	0.1474	56.0524	11.3216	143.1664
17	1.4212	0.4074	0.083	3.6557	-0.3678	3.4889	0.0467	0.0921	-0.1137	-0.0972	-0.0147	0.0866	0.1267	-0.023	-0.031	0.0979	-0.0031	-0.0088	0.078	-0.0126	0.0853	45.1369	5.3106	138.3515
18	0.9582	0.5464	-0.4867	3.2337	-1.5008	1.9307	-0.0219	-0.0206	0.0967	0.158	0.1636	0.269	-0.1367	-0.184	-0.1114	0.0667	0.0126	0.0033	0.1301	-0.0096	0.1055	37.3784	21.2172	144.2168
19	3.2594	-3.1967	0.3929	4.5601	-1.1717	3.9898	0.0327	0.1107	0.4814	-0.0962	0.0234	0.2556	-0.256	-0.2791	-0.0331	0.0953	-0.0172	-0.0391	0.1295	0.0254	0.2767	31.8	28.7077	134.5773
20	2.8166	-0.3811	0.2637	1.9512	-0.1333	1.6624	-0.039	0.0534	0.1245	-0.1634	0.0524	0.2549	-0.0489	-0.1591	0.0085	0.1094	0.0058	-0.0235	0.097	0.0163	0.1416	36.7443	26.7991	135.0887
21	3.9372	2.4273	-0.7646	5.8114	-1.1859	8.0154	-0.1548	0.0706	0.0746	-0.1085	0.1034	-0.0969	-0.0532	0.087	0.0364	0.1054	0.0106	-0.0075	0.0579	-0.0129	0.1015	44.5629	34.177	138.5383

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN 'A' AND (RESID 204 THROUGH 220 )
2	X-RAY DIFFRACTION	2	CHAIN 'A' AND (RESID 221 THROUGH 237 )
3	X-RAY DIFFRACTION	3	CHAIN 'A' AND (RESID 238 THROUGH 251 )
4	X-RAY DIFFRACTION	4	CHAIN 'B' AND (RESID 26 THROUGH 43 )
5	X-RAY DIFFRACTION	5	CHAIN 'B' AND (RESID 44 THROUGH 84 )
6	X-RAY DIFFRACTION	6	CHAIN 'B' AND (RESID 85 THROUGH 251 )
7	X-RAY DIFFRACTION	7	CHAIN 'C' AND (RESID 27 THROUGH 43 )
8	X-RAY DIFFRACTION	8	CHAIN 'C' AND (RESID 44 THROUGH 65 )
9	X-RAY DIFFRACTION	9	CHAIN 'C' AND (RESID 66 THROUGH 94 )
10	X-RAY DIFFRACTION	10	CHAIN 'C' AND (RESID 95 THROUGH 180 )
11	X-RAY DIFFRACTION	11	CHAIN 'C' AND (RESID 181 THROUGH 220 )
12	X-RAY DIFFRACTION	12	CHAIN 'C' AND (RESID 221 THROUGH 237 )
13	X-RAY DIFFRACTION	13	CHAIN 'C' AND (RESID 238 THROUGH 250 )
14	X-RAY DIFFRACTION	14	CHAIN 'D' AND (RESID 1 THROUGH 3 )
15	X-RAY DIFFRACTION	15	CHAIN 'A' AND (RESID 27 THROUGH 43 )
16	X-RAY DIFFRACTION	16	CHAIN 'A' AND (RESID 44 THROUGH 65 )
17	X-RAY DIFFRACTION	17	CHAIN 'A' AND (RESID 66 THROUGH 94 )
18	X-RAY DIFFRACTION	18	CHAIN 'A' AND (RESID 95 THROUGH 128 )
19	X-RAY DIFFRACTION	19	CHAIN 'A' AND (RESID 129 THROUGH 143 )
20	X-RAY DIFFRACTION	20	CHAIN 'A' AND (RESID 144 THROUGH 193 )
21	X-RAY DIFFRACTION	21	CHAIN 'A' AND (RESID 194 THROUGH 203 )

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