PDB-3d9b: Symmetric structure of E. coli AcrB

ID or keywords:

Entry

Database: PDB / ID: 3d9b

Title

Symmetric structure of E. coli AcrB

Components

Acriflavine resistance protein B

Keywords

TRANSPORT PROTEIN / alpha-helices / transmembrane protein / Inner membrane / Transport

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: 3.42 Å

Authors

Veesler, D. / Blangy, S. / Cambillau, C. / Sciara, G.

Citation

Journal: Acta Crystallogr.,Sect.F / Year: 2008
Title: There is a baby in the bath water: AcrB contamination is a major problem in membrane-protein crystallization.
Authors: Veesler, D. / Blangy, S. / Cambillau, C. / Sciara, G.

History

Deposition	May 27, 2008	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 1, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2	Mar 21, 2012	Group: Database references
Revision 1.3	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_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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	3d9b.cif.gz	208.5 KB	Display	PDBx/mmCIF format
PDB format	pdb3d9b.ent.gz	165.6 KB	Display	PDB format
PDBx/mmJSON format	3d9b.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3d9b_validation.pdf.gz	437.1 KB	Display	wwPDB validaton report
Full document	3d9b_full_validation.pdf.gz	483.1 KB	Display
Data in XML	3d9b_validation.xml.gz	42.2 KB	Display
Data in CIF	3d9b_validation.cif.gz	56.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/d9/3d9b ftp://data.pdbj.org/pub/pdb/validation_reports/d9/3d9b	HTTPS FTP

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Related structure data

Related structure data	2i6wS S: Starting model for refinement
Similar structure data	3w9i-2 4zln-1 2gif-d 5yil-d 3w9j-1 2hrt-2 2i6w-1 2v50-1 3w9j-2 4zjl-1 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

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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)

Deposited unit

A: Acriflavine resistance protein B

hetero molecules

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

1

A: Acriflavine resistance protein B

hetero molecules

A: Acriflavine resistance protein B

hetero molecules

A: Acriflavine resistance protein B

hetero molecules

defined by author&software
341 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	145.740, 145.740, 514.000
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	155
Space group name H-M	H32

Components on special symmetry positions

ID	Model	Components
1	1	A-1201- NI

#1: Protein	Acriflavine resistance protein B Mass: 113665.180 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: BL21(DE3) / References: UniProt: P31224
#2: Chemical	ChemComp-NI / NICKEL (II) ION Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 4.62 Å³/Da / Density % sol: 73.38 % Description: The total number of all reflections collected is 176182
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.6 Details: 0.1M MES, 31% PEG 400, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9798 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 10, 2007
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9798 Å / Relative weight: 1
Reflection	Resolution: 3.42→20 Å / Num. obs: 28788 / % possible obs: 99.3 % / Observed criterion σ(I): 3 / Redundancy: 6.12 % / B_iso Wilson estimate: 67.7 Å² / R_merge(I) obs: 0.124 / R_sym value: 0.124 / Net I/σ(I): 11.97
Reflection shell	Resolution: 3.42→3.6 Å / Redundancy: 6.24 % / R_merge(I) obs: 0.619 / Mean I/σ(I) obs: 3.25 / Num. unique all: 4072 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
ADSC	Quantum	data collection
XDS		data reduction
XSCALE		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 2I6W

2i6w

Resolution: 3.42→19.97 Å / Cor.coef. F_o:F_c: 0.871 / Cor.coef. F_o:F_c free: 0.802 / SU B: 87.26 / SU ML: 0.634 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.656 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.35459	1152	4 %	RANDOM
R_work	0.28851	-	-	-
obs	0.29114	27636	100 %	-
all	-	28788	-	-

Solvent computation

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

Displacement parameters

B_iso mean: 44.522 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.1 Å²	0.05 Å²	0 Å²
2-	-	0.1 Å²	0 Å²
3-	-	-	-0.15 Å²

Refine analyze

Luzzati coordinate error free: 0.656 Å

Refinement step

Cycle: LAST / Resolution: 3.42→19.97 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7950	0	1	0	7951

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.022	8018
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	5236
X-RAY DIFFRACTION	r_angle_refined_deg	1.408	1.964	10905
X-RAY DIFFRACTION	r_angle_other_deg	1.075	3	12823
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	8.433	5	1044
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	39.052	24.652	316
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.867	15	1302
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	13.982	15	35
X-RAY DIFFRACTION	r_chiral_restr	0.19	0.2	1285
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	8994
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1580
X-RAY DIFFRACTION	r_nbd_refined	0.252	0.2	2362
X-RAY DIFFRACTION	r_nbd_other	0.2	0.2	5523
X-RAY DIFFRACTION	r_nbtor_refined	0.19	0.2	3976
X-RAY DIFFRACTION	r_nbtor_other	0.088	0.2	4227
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.194	0.2	247
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.149	0.2	4
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.262	0.2	64
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.262	0.2	88
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.112	0.2	8
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	0.639	1.5	6650
X-RAY DIFFRACTION	r_mcbond_other	0.058	1.5	2133
X-RAY DIFFRACTION	r_mcangle_it	0.698	2	8325
X-RAY DIFFRACTION	r_scbond_it	0.615	3	3277
X-RAY DIFFRACTION	r_scangle_it	0.951	4.5	2580
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 3.42→3.506 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.394	82	-
R_work	0.341	1961	-
obs	-	-	100 %

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	10.247	2.4087	8.8827	3.2058	6.1433	13.9303	-0.7213	0.3904	0.3238	-0.2555	-0.5542	-0.924	1.7532	0.0614	1.2755	-0.1324	0.434	0.2552	0.0266	0.5309	-0.2062	61.0176	27.9102	21.2523
2	4.3656	-0.4832	-3.9692	0.3285	1.3528	6.6431	0.7366	0.5584	0.1216	0.2903	-0.1287	-0.2655	0.2735	-0.5715	-0.6078	0.001	0.2712	0.0013	-0.1756	0.1975	0.301	55.0897	44.8282	68.322
3	1.0051	2.2064	1.5534	5.2723	2.2206	5.6986	-0.1711	-0.0662	-0.5153	-0.0786	-0.0723	-0.1813	0.1417	1.0599	0.2434	-0.0833	0.1826	0.0521	0.0719	-0.09	-0.1741	61.3982	51.2284	70.068
4	1.8494	2.4356	1.7158	5.4982	3.0433	4.001	0.3769	0.1475	0.1512	-0.0921	-0.0179	-0.4288	0.06	0.2905	-0.359	-0.1123	0.2521	0.0189	0.091	0.0834	-0.2434	55.6654	33.9731	75.1268
5	2.7318	-0.0092	-0.1793	0.535	-0.5596	0.5983	0.317	-0.5725	-0.3785	0.0554	-0.0834	0.0517	-0.272	0.175	-0.2336	0.0042	-0.0206	-0.0247	0.0041	0.0808	-0.4766	65.4675	25.5536	97.2246
6	9.1529	-0.0923	7.5291	3.2871	0.1896	10.4731	0.1772	-0.6773	-0.5124	0.6795	0.113	0.2459	0.4268	-0.8582	-0.2902	-0.0952	-0.1176	0.2815	-0.1034	0.2088	-0.7135	51.1298	26.0303	98.0341
7	8.1205	-6.0586	2.6877	4.5203	-2.0053	0.8896	1.5285	1.6216	-0.2501	-0.43	-1.461	-0.4178	0.6931	1.0315	-0.0675	0.1143	0.1938	-0.0558	0.3703	0.0388	-0.2563	48.0485	25.6651	63.3234
8	6.0342	-1.126	0.277	5.5153	0.3752	6.6644	-0.3062	-0.3832	-0.3278	0.2301	0.3076	-0.7075	1.5946	0.6548	-0.0014	-0.2199	0.1205	0.002	-0.0861	-0.0856	-0.3743	45.2772	30.5537	27.1918
9	1.5486	-0.4177	-2.9783	2.3451	1.0676	5.7592	-0.3506	-0.6586	0.9035	-0.3261	-0.3716	-0.2551	0.2379	0.8478	0.7221	-0.4505	0.2261	-0.1409	0.249	0.1708	0.6116	50.5361	41.4982	21.7569
10	0.7665	-0.7494	-1.0911	5.5286	-2.1876	4.7715	-0.0022	-0.0878	0.197	-0.8955	-0.2679	-0.3577	0.6735	-0.0301	0.2701	-0.6942	0.1359	-0.0739	-0.076	0.1656	-0.4585	40.7678	39.4418	13.9228
11	0.0327	-0.1099	-0.0102	1.7502	-2.3638	4.1655	0.2301	-0.0873	0.2609	0.1759	0.0887	0.3009	-0.3279	-0.3112	-0.3188	-0.1361	-0.1157	-0.1338	0.1736	0.1476	-0.2507	32.564	45.9945	57.3628
12	8.169	-6.45	-12.2117	7.228	9.9143	18.2896	0.7924	0.5608	1.4121	-0.7331	1.0667	-0.6952	-1.4369	2.801	-1.8591	0.07	-0.1453	-0.2218	-0.0072	0.4043	-0.5421	38.8349	38.4184	70.8101
13	9.2352	2.1385	1.3083	9.9581	4.3925	8.1249	0.4914	1.4343	0.7386	-0.1921	-0.0337	-0.0297	-0.6284	-0.5055	-0.4577	-0.1675	0.1081	-0.1993	-0.182	0.2938	-0.4499	30.7921	41.8568	60.9
14	0.0585	0.1549	-0.6069	2.9899	-2.6272	6.6992	0.051	-0.2328	0.5271	0.3231	-0.2269	0.8325	-1.116	-0.3304	0.1759	-0.313	0.1082	0.1645	-0.0485	-0.1755	0.2015	44.7721	61.9848	80.989
15	4.6286	-2.6853	0.1859	9.8675	1.902	0.7256	0.095	-0.7594	-0.042	0.3622	-0.2341	0.2363	-0.0775	-0.1976	0.1391	-0.1004	-0.1456	0.1723	-0.0333	0.0216	-0.7838	52.4619	37.1383	97.8082
16	0.5766	-0.8937	-0.3424	1.385	0.5306	0.2033	0.5173	-0.0355	0.4717	0.3996	-0.1121	0.5877	-0.0891	0.3484	-0.4051	-0.0907	-0.1446	0.1497	0.0756	-0.1368	-0.0609	49.5173	54.7433	91.331
17	11.9651	-2.328	5.3788	6.0667	-2.0032	10.292	-0.4094	1.9012	0.6021	-0.8774	0.0677	0.6693	-1.4699	-0.1615	0.3417	-0.3583	0.1004	-0.006	-0.0712	0.1299	-0.1196	44.5715	66.7959	62.3663
18	4.0431	-0.3387	-1.0011	8.3184	2.5009	0.9525	-0.107	-0.2169	0.6063	0.7907	1.4743	-0.2143	-0.6873	3.5726	-1.3672	-0.1531	0.0631	0.2499	0.7137	-0.6391	0.2687	51.9116	59.9875	28.4823
19	1.5486	0.1201	1.8754	1.2102	-0.9066	11.2111	0.0677	0.1552	0.1712	-0.0064	0.184	-0.2187	-0.2877	0.2658	-0.2517	-0.4322	0.0174	-0.1823	-0.1963	-0.0126	-0.0338	41.5588	51.3205	20.4082
20	2.8057	-0.4519	2.7573	1.1398	1.0182	4.714	0.373	0.1724	0.1244	0.0836	0.3933	-0.7282	-0.5085	-0.4757	-0.7663	-0.2426	0.1226	-0.1528	-0.2824	-0.1527	-0.2811	39.6039	51.1297	19.6796

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	1 - 28	1 - 28
2	X-RAY DIFFRACTION	2	A	A	29 - 59	29 - 59
3	X-RAY DIFFRACTION	3	A	A	60 - 106	60 - 106
4	X-RAY DIFFRACTION	4	A	A	107 - 177	107 - 177
5	X-RAY DIFFRACTION	5	A	A	178 - 240	178 - 240
6	X-RAY DIFFRACTION	6	A	A	241 - 284	241 - 284
7	X-RAY DIFFRACTION	7	A	A	285 - 337	285 - 337
8	X-RAY DIFFRACTION	8	A	A	338 - 389	338 - 389
9	X-RAY DIFFRACTION	9	A	A	390 - 465	390 - 465
10	X-RAY DIFFRACTION	10	A	A	466 - 539	466 - 539
11	X-RAY DIFFRACTION	11	A	A	540 - 615	540 - 615
12	X-RAY DIFFRACTION	12	A	A	616 - 633	616 - 633
13	X-RAY DIFFRACTION	13	A	A	634 - 677	634 - 677
14	X-RAY DIFFRACTION	14	A	A	678 - 740	678 - 740
15	X-RAY DIFFRACTION	15	A	A	741 - 792	741 - 792
16	X-RAY DIFFRACTION	16	A	A	793 - 829	793 - 829
17	X-RAY DIFFRACTION	17	A	A	830 - 865	830 - 865
18	X-RAY DIFFRACTION	18	A	A	866 - 900	866 - 900
19	X-RAY DIFFRACTION	19	A	A	901 - 974	901 - 974
20	X-RAY DIFFRACTION	20	A	A	975 - 1044	975 - 1044

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