PDB-2gif: Asymmetric structure of trimeric AcrB from Escherichia coli

ID or keywords:

Entry

Database: PDB / ID: 2gif

Title

Asymmetric structure of trimeric AcrB from Escherichia coli

Components

Acriflavine resistance protein B

Keywords

MEMBRANE PROTEIN/TRANSPORT PROTEIN / membrane protein / secondary transport / RND / antibiotic resistance / drug-efflux pump / alternating site mechanism / MEMBRANE PROTEIN-TRANSPORT PROTEIN COMPLEX

Function / homology

Function and homology information

xenobiotic detoxification by transmembrane export across the cell outer membrane / efflux pump complex / periplasmic side of plasma membrane / efflux transmembrane transporter activity / xenobiotic transmembrane transporter activity / outer membrane-bounded periplasmic space / identical protein binding / membrane / plasma membrane
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.9 Å

Authors

Seeger, M.A. / Schiefner, A. / Eicher, T. / Verrey, F. / Diederichs, K. / Pos, K.M.

Citation

Journal: Science / Year: 2006
Title: Structural Asymmetry of AcrB Trimer Suggests a Peristaltic Pump Mechanism.
Authors: Seeger, M.A. / Schiefner, A. / Eicher, T. / Verrey, F. / Diederichs, K. / Pos, K.M.

History

Deposition	Mar 28, 2006	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 12, 2006	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.3	Oct 18, 2017	Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4	Aug 30, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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	2gif.cif.gz	568.1 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	2gif_validation.pdf.gz	483.1 KB	Display	wwPDB validaton report
Full document	2gif_full_validation.pdf.gz	547.5 KB	Display
Data in XML	2gif_validation.xml.gz	100.9 KB	Display
Data in CIF	2gif_validation.cif.gz	136.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gi/2gif ftp://data.pdbj.org/pub/pdb/validation_reports/gi/2gif	HTTPS FTP

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Related structure data

Related structure data	2hrtC 1iwgS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4zln-1 3d9b-1 5yil-d 2hrt-2 4zjl-1 3w9i-2 2v50-1 2hqd-1 2i6w-1 4zjq-1 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
Related items in Molecule of the Month	#95 - Nov 2007 Multidrug Resistance Transporters similarity (5) #129 - Sep 2010 Isocitrate Dehydrogenase similarity (1) #154 - Oct 2012 Citric Acid Cycle similarity (1) #191 - Nov 2015 Glutamate-gated Chloride Receptors similarity (1) #215 - Nov 2017 Aspartate Transcarbamoylase similarity (1) #258 - Jun 2021 Glucocorticoid Receptor and Dexamethasone similarity (1) #89 - May 2007 Aconitase and Iron Regulatory Protein 1 similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#95 - Nov 2007
Multidrug Resistance Transporters
similarity (5)
#129 - Sep 2010
Isocitrate Dehydrogenase
similarity (1)
#154 - Oct 2012
Citric Acid Cycle
similarity (1)
#191 - Nov 2015
Glutamate-gated Chloride Receptors
similarity (1)
#215 - Nov 2017
Aspartate Transcarbamoylase
similarity (1)
#258 - Jun 2021
Glucocorticoid Receptor and Dexamethasone
similarity (1)
#89 - May 2007
Aconitase and Iron Regulatory Protein 1
similarity (1)

Deposited unit

A: Acriflavine resistance protein B

B: Acriflavine resistance protein B

C: Acriflavine resistance protein B

hetero molecules

345 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)	222.800, 134.100, 161.010
Angle α, β, γ (deg.)	90.00, 98.21, 90.00
Int Tables number	5
Space group name H-M	C121

Details

Biological assembly is a trimer as found in the asymmetric unit.

#1: Protein	Acriflavine resistance protein B Mass: 114736.289 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: acrB, acrE / Plasmid: pET24 / Production host: Escherichia coli (E. coli) / Strain (production host): C43(DE3) / References: UniProt: P31224
#2: Chemical	ChemComp-FLC / CITRATE ANION Mass: 189.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₅O₇

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.46 Å³/Da / Density % sol: 64.42 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion / pH: 4.6 Details: 5% PEG 400, 16-22% PEG 300, 8-11% glycerol, 70mM sodium citrate, pH 4.6, VAPOR DIFFUSION, temperature 290K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
Detector	Type: MARRESEARCH / Detector: CCD / Date: Jan 29, 2005
Radiation	Monochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.9→30 Å / Num. all: 103912 / Num. obs: 103134 / % possible obs: 99.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.2 % / R_merge(I) obs: 0.073 / Net I/σ(I): 13.4
Reflection shell	Resolution: 2.9→3.08 Å / Redundancy: 4.2 % / R_merge(I) obs: 0.956 / Mean I/σ(I) obs: 1.6 / % possible all: 97

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0005	refinement
MAR345		data collection
XDS		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IWG

1iwg

Resolution: 2.9→29.51 Å / Cor.coef. F_o:F_c: 0.942 / Cor.coef. F_o:F_c free: 0.926 / SU B: 46.735 / SU ML: 0.381 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 1.67 / ESU R Free: 0.386 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.26677	5177	5 %	RANDOM
R_work	0.22551	-	-	-
obs	0.22761	98361	99.77 %	-
all	-	98361	-	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 73.945 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	6.21 Å²	0 Å²	4.25 Å²
2-	-	-3.26 Å²	0 Å²
3-	-	-	-1.74 Å²

Refinement step

Cycle: LAST / Resolution: 2.9→29.51 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	23624	0	26	0	23650

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.022	24101
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.061	1.968	32729
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.148	5	3105
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.386	24.535	946
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.854	15	4053
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.575	15	112
X-RAY DIFFRACTION	r_chiral_restr	0.069	0.2	3850
X-RAY DIFFRACTION	r_gen_planes_refined	0.002	0.02	17886
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.198	0.2	12389
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.301	0.2	16953
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.118	0.2	732
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.137	0.2	22
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.116	0.2	3
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.194	1.5	15777
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.35	2	24852
X-RAY DIFFRACTION	r_scbond_it	0.457	3	9314
X-RAY DIFFRACTION	r_scangle_it	0.783	4.5	7877
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.9→2.975 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.373	383	-
R_work	0.343	7154	-
obs	-	-	99.77 %

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	2.1692	0.5919	-1.845	1.7216	0.0889	2.2401	0.0184	-0.1703	-0.0311	0.3742	-0.022	0.454	0.0003	-0.711	0.0036	-0.1054	-0.0803	0.0824	0.4343	-0.0272	0.0592	-100.386	7.0646	-41.4258
2	5.0916	-1.7297	-3.4985	9.3067	1.5582	3.6404	-0.2727	-0.2757	-0.3219	0.0481	-0.0582	-0.0307	0.164	0.2081	0.3309	-0.573	0.0106	-0.3031	-0.4778	0.0665	-0.6301	-51.7494	4.2427	-55.9539
3	2.061	1.7647	-1.0568	5.837	-1.01	2.2467	0.0072	0.3481	-0.2241	-0.395	-0.0092	0.5301	-0.1173	-0.5377	0.002	-0.3571	0.033	-0.152	-0.3207	0.0093	-0.4157	-68.8159	14.2885	-73.0812
4	1.4116	1.5942	0.3469	2.8626	0.4419	2.0734	-0.1487	0.1921	-0.0701	-0.7604	-0.0864	-0.4873	-0.1645	0.2519	0.2351	-0.0399	-0.0143	0.2623	-0.4871	0.1362	-0.2291	-38.9543	25.1615	-81.9689
5	13.6376	0.3374	-3.8532	4.4903	-0.0015	4.2951	-0.1778	-0.2	-1.4298	0.0323	-0.2433	0.1879	0.9311	-0.898	0.4212	0.0639	-0.1892	0.0187	-0.2023	-0.1294	-0.0517	-74.121	-5.5474	-76.0597
6	5.7263	3.6528	0.0505	7.3556	-0.1718	3.9806	-0.1099	-0.2375	-0.82	0.1231	-0.134	0.4827	0.8213	-0.5961	0.2439	0.1582	-0.1085	0.2331	-0.468	0.0067	-0.137	-58.7533	-18.8737	-57.4653
7	1.6825	-1.8118	-0.3333	4.3245	0.4152	1.841	-0.0611	0.0898	-0.0582	-0.4516	0.0117	-0.7175	0.28	0.4986	0.0494	-0.0601	0.0847	0.2894	-0.4479	0.042	-0.2219	-36.6738	3.6525	-80.4419
8	1.1649	0.3996	-0.6047	1.2056	-0.4387	1.9049	-0.0607	-0.0525	-0.5154	-0.0314	-0.0459	0.4257	0.4879	-0.6409	0.1066	0.2142	-0.3733	0.1806	0.4104	-0.0089	0.2787	-102.8791	-12.5945	-39.1574
9	2.1434	-0.2296	-1.3853	1.6099	0.338	1.1878	0.0958	-0.3912	0.2153	0.2895	-0.0617	0.2481	-0.415	-0.2709	-0.0341	0.2106	0.233	0.2219	0.1905	-0.0962	-0.0229	-85.3148	38.8076	-21.2781
10	4.94	1.2331	-4.0791	1.7849	-1.6303	6.3053	0.2355	-0.4297	0.1211	0.3363	-0.2631	-0.2101	-0.6279	0.2034	0.0276	-0.2557	0.0492	-0.0961	-0.574	-0.0059	-0.434	-53.8797	27.248	-57.7248
11	5.4852	1.3399	-4.3988	3.0837	-1.4474	5.9354	0.0854	-0.5849	0.0549	0.4462	-0.0212	-0.1378	-0.5913	0.3576	-0.0642	0.1843	-0.0561	-0.0789	-0.1682	-0.1239	-0.0859	-44.41	43.7725	-37.0384
12	1.1995	-1.5859	1.1387	4.8493	-1.5892	1.1982	0.0303	-0.3479	0.1119	0.1651	-0.3067	-0.9203	-0.4385	1.0498	0.2763	-0.1959	-0.1696	-0.0633	0.0735	0.1419	0.1101	-19.18	29.0262	-53.4877
13	6.8997	-0.7872	-5.1063	1.5833	0.3799	5.1412	0.1144	0.072	0.553	0.0069	-0.0297	0.5831	-0.7624	-0.5422	-0.0847	0.4717	0.0295	0.0682	-0.2682	-0.0903	0.169	-55.2529	58.6469	-49.0261
14	5.9952	-2.3457	-0.5131	5.3773	0.3832	2.7059	0.1467	-0.2191	0.3681	-0.1715	0.0299	0.6529	-0.7248	-0.7368	-0.1766	-0.0218	0.2041	0.0067	-0.457	0.117	-0.1756	-69.2686	42.6638	-68.5203
15	1.598	0.2916	0.1461	1.2206	-1.3814	2.7835	0.0551	-0.083	0.1323	-0.3591	-0.1819	-0.7428	-0.0672	0.6228	0.1268	-0.0775	-0.1678	0.1475	-0.4035	0.0358	-0.0788	-30.5013	37.8735	-69.9169
16	2.2627	0.5033	-0.8471	1.2408	0.0314	1.0017	0.1297	-0.0043	0.5622	0.0583	-0.002	0.4716	-0.4684	-0.5726	-0.1277	0.2992	0.4382	0.2405	0.3434	0.0348	0.3257	-98.2766	47.3255	-33.5011
17	27.6111	1.2535	32.7575	16.9735	3.9869	39.2327	0.5338	-0.1338	-0.4593	-0.698	0.5133	-0.9344	2.2032	-0.9524	-1.047	0.445	0.0637	0.5046	0.4129	0.2809	0.7133	-125.476	35.0083	-29.6943
18	2.2939	0.568	-0.9969	1.5571	-0.4248	1.9128	-0.1523	-0.3708	-0.2016	0.4668	-0.011	0.3371	0.1268	-0.2503	0.1633	0.1417	0.0492	0.1085	0.2524	0.1353	-0.2709	-77.8867	-1.1021	-9.1237
19	10.8784	2.3014	-1.0834	2.3244	-1.6677	2.2892	-0.2896	-0.1738	0.2757	-0.051	0.0582	-0.446	-0.3481	0.4051	0.2314	-0.1576	-0.0227	-0.2664	-0.2791	0.0024	-0.3358	-43.3876	19.1419	-39.091
20	1.0656	-1.1741	-1.4966	4.4116	0.8518	4.0271	-0.319	-0.3621	-0.3962	0.4389	-0.0077	-0.2591	0.7844	0.3615	0.3267	-0.0789	0.1067	-0.0981	-0.1466	0.2895	-0.1122	-41.8976	-8.8114	-36.9241
21	1.2549	0.0131	0.6563	1.4953	0.5845	3.4132	-0.0953	0.0439	-0.4696	-0.2228	0.1169	-0.8187	0.3046	1.0196	-0.0216	-0.1325	0.1718	0.2324	-0.2147	0.1022	0.0859	-25.7672	-3.1814	-65.0639
22	5.5514	0.5336	-1.118	2.4289	-0.7768	2.8767	0.0225	-0.6881	-0.0455	0.9897	-0.0963	-0.4696	-0.048	0.4237	0.0739	0.1702	0.2013	-0.3122	0.3187	0.2375	-0.0504	-33.0466	-3.4583	-18.7362
23	2.9024	-2.5853	-1.5469	3.0026	2.2887	4.2944	0.0755	-0.9904	0.1547	0.4164	-0.3078	-0.432	-0.1707	0.6978	0.2323	-0.0369	-0.0762	-0.4837	0.4901	0.0259	-0.1875	-35.0116	19.2787	-16.8231
24	3.4285	0.3847	0.8368	2.7064	0.9587	1.6456	-0.2257	-0.2103	0.0641	-0.1981	0.1727	-1.0822	-0.0086	1.0423	0.0529	-0.3183	0.0733	-0.0018	0.2091	0.1638	0.1839	-16.0224	9.679	-50.5677
25	2.4625	0.2144	-1.718	1.184	-0.1308	2.9137	0.1128	-0.7163	-0.0085	0.6882	-0.124	0.2321	-0.1668	0.0529	0.0112	0.3726	0.034	0.0324	0.4868	0.0319	-0.2906	-71.072	10.91	5.4936

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	2 - 40	2 - 40
2	X-RAY DIFFRACTION	1	A	A	325 - 502	325 - 502
3	X-RAY DIFFRACTION	2	A	A	41 - 133	41 - 133
4	X-RAY DIFFRACTION	3	A	A	134 - 180	134 - 180
5	X-RAY DIFFRACTION	3	A	A	272 - 324	272 - 324
6	X-RAY DIFFRACTION	4	A	A	181 - 271	181 - 271
7	X-RAY DIFFRACTION	5	A	A	570 - 672	570 - 672
8	X-RAY DIFFRACTION	6	A	A	673 - 723	673 - 723
9	X-RAY DIFFRACTION	6	A	A	812 - 859	812 - 859
10	X-RAY DIFFRACTION	7	A	A	724 - 811	724 - 811
11	X-RAY DIFFRACTION	8	A	A	503 - 569	503 - 569
12	X-RAY DIFFRACTION	8	A	A	860 - 1033	860 - 1033
13	X-RAY DIFFRACTION	9	B	B	2 - 40	2 - 40
14	X-RAY DIFFRACTION	9	B	B	325 - 502	325 - 502
15	X-RAY DIFFRACTION	10	B	B	41 - 133	41 - 133
16	X-RAY DIFFRACTION	11	B	B	134 - 180	134 - 180
17	X-RAY DIFFRACTION	11	B	B	272 - 324	272 - 324
18	X-RAY DIFFRACTION	12	B	B	181 - 271	181 - 271
19	X-RAY DIFFRACTION	13	B	B	570 - 672	570 - 672
20	X-RAY DIFFRACTION	14	B	B	673 - 723	673 - 723
21	X-RAY DIFFRACTION	14	B	B	812 - 859	812 - 859
22	X-RAY DIFFRACTION	15	B	B	724 - 811	724 - 811
23	X-RAY DIFFRACTION	16	B	B	503 - 569	503 - 569
24	X-RAY DIFFRACTION	16	B	B	860 - 1033	860 - 1033
25	X-RAY DIFFRACTION	17	B	B	1034 - 1045	1034 - 1045
26	X-RAY DIFFRACTION	18	C	C	2 - 40	2 - 40
27	X-RAY DIFFRACTION	18	C	C	325 - 502	325 - 502
28	X-RAY DIFFRACTION	19	C	C	41 - 133	41 - 133
29	X-RAY DIFFRACTION	20	C	C	134 - 180	134 - 180
30	X-RAY DIFFRACTION	20	C	C	272 - 324	272 - 324
31	X-RAY DIFFRACTION	21	C	C	181 - 271	181 - 271
32	X-RAY DIFFRACTION	22	C	C	570 - 672	570 - 672
33	X-RAY DIFFRACTION	23	C	C	673 - 723	673 - 723
34	X-RAY DIFFRACTION	23	C	C	812 - 859	812 - 859
35	X-RAY DIFFRACTION	24	C	C	724 - 811	724 - 811
36	X-RAY DIFFRACTION	25	C	C	503 - 569	503 - 569
37	X-RAY DIFFRACTION	25	C	C	860 - 1033	860 - 1033

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