PDB-5j4i: Crystal Structure of the L-arginine/agmatine antiporter from E. c...

ID or keywords:

Entry

Database: PDB / ID: 5j4i

Title

Crystal Structure of the L-arginine/agmatine antiporter from E. coli at 2.2 Angstroem resolution

Components

Arginine/agmatine antiporter

Keywords

TRANSPORT PROTEIN /

AdiC /

Transporter /

Membrane Protein

Function / homology

Function and homology information

arginine:agmatine antiporter activity / L-arginine transmembrane transporter activity / amino acid transmembrane transport / intracellular pH elevation / amino acid transport /

antiporter activity / identical protein binding /

plasma membrane
Similarity search - Function

Biological species

Escherichia coli O157:H7 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.207 Å

Authors

Jeckelmann, J.M. / Ilgue, H. / Fotiadis, D.

Funding support

Switzerland, 1items

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Insights into the molecular basis for substrate binding and specificity of the wild-type L-arginine/agmatine antiporter AdiC.
Authors: Ilgu, H. / Jeckelmann, J.M. / Gapsys, V. / Ucurum, Z. / de Groot, B.L. / Fotiadis, D.

History

Deposition	Apr 1, 2016	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Aug 31, 2016	Provider: repository / Type: Initial release
Revision 1.1	Sep 14, 2016	Group: Database references
Revision 1.2	Sep 21, 2016	Group: Database references
Revision 1.3	Sep 6, 2017	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4	Jan 10, 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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PDBx/mmCIF format	5j4i.cif.gz	335.4 KB	Display	PDBx/mmCIF format
PDB format	pdb5j4i.ent.gz	276 KB	Display	PDB format
PDBx/mmJSON format	5j4i.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/j4/5j4i ftp://data.pdbj.org/pub/pdb/validation_reports/j4/5j4i	HTTPS FTP

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Related structure data

Related structure data	5j4nC 3ob6S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3ob6-d 5j4n-d 3lrc-2 5why-d 3lrb-d 2nnb-d 7nqu-d 3lrc-1 6rzq-d 1jpz-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: Arginine/agmatine antiporter

B: Arginine/agmatine antiporter

95.7 kDa, 2 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)	104.739, 175.424, 73.148
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

#1: Protein	Arginine/agmatine antiporter Mass: 47841.387 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Gene: adiC, Z5717, ECs5097 / Plasmid: pET21 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P60063, UniProt: P60061*PLUS
#2: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 159 / 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: 3.35 Å³/Da / Density % sol: 63.3 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion / pH: 7 / Details: PEG 400, NaCl

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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 PILATUS3 6M / Detector: PIXEL / Date: Mar 28, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.207→49.51 Å / Num. obs: 68197 / % possible obs: 99.4 % / Redundancy: 5.9 % / R_merge(I) obs: 0.071 / Net I/σ(I): 14.9
Reflection shell	Resolution: 2.21→2.33 Å / Redundancy: 5.5 % / R_merge(I) obs: 1.14 / Mean I/σ(I) obs: 1.5 / % possible all: 96.8

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
XDS	VERSION November 11, 2013	data reduction
XSCALE	VERSION November 11, 2013	data scaling
MOLREP	Phaser	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3OB6

3ob6

Resolution: 2.207→49.505 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.06 / Phase error: 22.54

	R_factor	Num. reflection	% reflection
R_free	0.2101	6480	5 %
R_work	0.1972	-	-
obs	0.1978	68197	99.02 %

Solvent computation

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

Displacement parameters

B_iso mean: 60.1 Å²

Refinement step

Cycle: LAST / Resolution: 2.207→49.505 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6480	0	0	159	6639

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	6652
X-RAY DIFFRACTION	f_angle_d	0.996	9106
X-RAY DIFFRACTION	f_dihedral_angle_d	10.791	2230
X-RAY DIFFRACTION	f_chiral_restr	0.044	1096
X-RAY DIFFRACTION	f_plane_restr	0.005	1108

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 (%)
2.2069-2.232	0.4029	176	0.3959	3439	X-RAY DIFFRACTION	82
2.232-2.2582	0.3393	212	0.332	4082	X-RAY DIFFRACTION	99
2.2582-2.2858	0.31	222	0.3185	4166	X-RAY DIFFRACTION	99
2.2858-2.3147	0.3326	214	0.312	4037	X-RAY DIFFRACTION	99
2.3147-2.3451	0.3044	214	0.2728	4132	X-RAY DIFFRACTION	100
2.3451-2.3773	0.291	219	0.2641	4180	X-RAY DIFFRACTION	100
2.3773-2.4112	0.289	215	0.2624	4117	X-RAY DIFFRACTION	100
2.4112-2.4472	0.2801	218	0.2623	4101	X-RAY DIFFRACTION	100
2.4472-2.4855	0.2683	216	0.241	4170	X-RAY DIFFRACTION	100
2.4855-2.5262	0.2428	215	0.2389	4143	X-RAY DIFFRACTION	100
2.5262-2.5698	0.2227	216	0.2261	4131	X-RAY DIFFRACTION	100
2.5698-2.6165	0.2111	222	0.211	4191	X-RAY DIFFRACTION	100
2.6165-2.6668	0.2382	212	0.2091	4102	X-RAY DIFFRACTION	100
2.6668-2.7212	0.2464	211	0.2019	4164	X-RAY DIFFRACTION	100
2.7212-2.7804	0.2268	218	0.1919	4122	X-RAY DIFFRACTION	100
2.7804-2.8451	0.1944	220	0.1907	4119	X-RAY DIFFRACTION	99
2.8451-2.9162	0.2208	214	0.1852	4162	X-RAY DIFFRACTION	100
2.9162-2.9951	0.2319	216	0.184	4103	X-RAY DIFFRACTION	100
2.9951-3.0832	0.2208	219	0.1834	4135	X-RAY DIFFRACTION	100
3.0832-3.1827	0.1862	222	0.1914	4191	X-RAY DIFFRACTION	100
3.1827-3.2964	0.2259	217	0.1925	4121	X-RAY DIFFRACTION	100
3.2964-3.4284	0.1883	215	0.1836	4110	X-RAY DIFFRACTION	100
3.4284-3.5844	0.1737	218	0.1765	4152	X-RAY DIFFRACTION	100
3.5844-3.7733	0.2099	217	0.1793	4131	X-RAY DIFFRACTION	100
3.7733-4.0096	0.2091	215	0.1927	4149	X-RAY DIFFRACTION	100
4.0096-4.319	0.1826	225	0.1801	4122	X-RAY DIFFRACTION	99
4.319-4.7533	0.1757	218	0.1664	4127	X-RAY DIFFRACTION	100
4.7533-5.4404	0.1921	220	0.1763	4106	X-RAY DIFFRACTION	100
5.4404-6.8514	0.2119	222	0.2017	4106	X-RAY DIFFRACTION	99
6.8514-49.5179	0.1895	222	0.1908	4093	X-RAY DIFFRACTION	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	8.4801	-3.4783	-0.2462	8.7381	1.6287	7.5744	0.1062	-0.2161	0.8018	-0.0245	0.1026	-0.2155	-0.9188	-0.3753	-0.1865	0.3859	0.0685	0.0138	0.445	-0.0664	0.3544	-21.6125	37.7736	0.755
2	3.3129	-0.2134	-1.5271	6.3029	-1.8014	1.3211	-0.1895	-0.3486	-0.2432	0.1088	0.0384	0.2226	0.1819	-0.154	0.159	0.4635	0.0694	0.018	0.511	-0.0417	0.3807	-11.642	13.7203	7.8533
3	3.2808	0.2645	0.0419	1.2617	-0.0811	2.3248	-0.0474	-0.1433	0.2023	-0.0291	0.0684	0.1027	0.2006	-0.139	-0.0232	0.3664	0.0695	-0.0027	0.3106	-0.0245	0.3385	-18.8949	28.3801	-6.875
4	1.9459	-1.0144	0.3659	7.6126	-2.1433	1.4616	-0.0996	-0.4321	0.1094	0.5371	0.3269	0.3073	-0.0051	-0.2664	-0.2421	0.4617	0.0508	-0.0221	0.5445	-0.0793	0.2704	-14.6424	18.4234	8.6501
5	5.2195	-6.3598	-1.4984	9.3661	2.2729	4.1736	-0.8015	-0.8412	-3.6535	0.2911	0.5633	2.4469	1.0337	-0.3814	0.3089	0.8971	-0.0252	0.072	0.7834	0.295	1.6864	-29.7676	7.1474	4.869
6	8.0496	6.2649	-5.0782	7.7723	-5.3612	4.7389	-0.0022	0.2033	0.5848	-0.2161	0.1495	0.4014	-0.141	-0.1991	-0.1957	0.3834	0.0593	-0.0835	0.382	-0.0286	0.3861	-19.0761	32.4111	-10.5666
7	5.0449	2.8925	-0.2293	9.0427	5.5391	6.7299	-0.0503	0.189	-0.3818	0.0545	0.1385	-0.2981	0.7285	0.0635	-0.1026	0.4462	0.0507	-0.0713	0.5098	0.051	0.341	-21.2944	27.5874	-19.1975
8	2.4021	0.0286	-0.8294	3.1552	-0.3854	3.8089	-0.0539	-0.105	0.4173	-0.0337	0.0133	0.0764	-0.113	-0.0647	0.0493	0.1934	0.0271	-0.055	0.3445	-0.035	0.3841	1.1921	30.0751	-8.6324
9	6.4679	2.0168	5.4996	5.3568	-0.3471	5.9786	-0.2566	0.7492	2.8406	-0.4289	0.5371	-3.489	-2.8204	2.8912	-0.2232	0.9568	-0.2782	0.1554	0.9653	-0.1429	1.3235	39.6239	35.863	-22.1882
10	6.2763	3.8598	2.4141	8.0187	0.8033	1.0207	-0.3019	0.3002	0.1924	-0.3118	0.1904	-0.2766	-0.04	0.242	0.0897	0.4243	-0.0583	0.0996	0.5127	-0.0108	0.5017	31.2164	23.4332	-27.5638
11	1.2245	0.7339	0.3224	7.7563	2.4968	1.4768	-0.0443	0.2072	0.1029	-0.5797	0.1258	-0.2749	-0.1434	0.1142	-0.0717	0.4778	-0.0301	0.0946	0.5518	0.0409	0.4109	17.2571	18.6509	-31.2369
12	3.0862	-0.8023	0.4696	1.2873	-0.0573	3.2117	-0.0356	0.1216	0.1269	0.0837	0.0712	-0.1877	0.4633	0.1461	-0.0454	0.3571	-0.0913	0.0503	0.326	-0.0541	0.3817	29.155	16.9575	-17.1879
13	1.9852	1.5667	1.8315	5.0418	2.9838	2.4582	0.0373	0.4085	0.0417	-0.3981	0.1806	-0.2825	0.0361	0.1833	-0.2321	0.4562	-0.031	0.0436	0.4559	0.0775	0.3002	17.0507	11.0088	-32.3915
14	2.0041	1.5805	0.5322	9.2851	3.4861	1.7471	-0.0052	0.2411	-0.0059	-0.4037	0.097	-0.4032	-0.0242	0.1797	-0.1095	0.4028	-0.0291	0.0632	0.5045	0.014	0.3188	23.7743	12.4022	-33.3153
15	3.3881	-0.3521	0.4196	1.2113	0.5154	1.7365	0.0211	0.02	0.0239	0.0057	0.0074	-0.2747	0.0986	0.0547	-0.0123	0.4024	-0.0684	0.0769	0.3676	-0.0276	0.4191	22.4813	20.8996	-18.159
16	3.2117	1.0424	1.0291	3.98	-0.1494	5.1491	0.0493	-0.1784	0.6203	0.5256	0.0751	-0.1332	-0.0589	0.3527	-0.1275	0.1976	0.0015	0.0275	0.3933	-0.0781	0.4201	7.605	30.4336	-5.619

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 5:23)
2	X-RAY DIFFRACTION	2	(chain A and resid 27:53)
3	X-RAY DIFFRACTION	3	(chain A and resid 54:167)
4	X-RAY DIFFRACTION	4	(chain A and resid 168:255)
5	X-RAY DIFFRACTION	5	(chain A and resid 256:275)
6	X-RAY DIFFRACTION	6	(chain A and resid 276:316)
7	X-RAY DIFFRACTION	7	(chain A and resid 317:347)
8	X-RAY DIFFRACTION	8	(chain A and resid 348:441)
9	X-RAY DIFFRACTION	9	(chain B and resid 5:10)
10	X-RAY DIFFRACTION	10	(chain B and resid 11:23)
11	X-RAY DIFFRACTION	11	(chain B and resid 27:69)
12	X-RAY DIFFRACTION	12	(chain B and resid 70:170)
13	X-RAY DIFFRACTION	13	(chain B and resid 171:219)
14	X-RAY DIFFRACTION	14	(chain B and resid 220:260)
15	X-RAY DIFFRACTION	15	(chain B and resid 261:401)
16	X-RAY DIFFRACTION	16	(chain B and resid 402:441)

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