PDB-6h7v: Crystal structure of BauA, the Ferric preacinetobactin receptor f...

ID or keywords:

Entry

Database: PDB / ID: 6h7v

Title

Crystal structure of BauA, the Ferric preacinetobactin receptor from Acinetobacter baumannii

Components

Ligand-gated channel protein

Ligand-gated ion channel

Keywords

MEMBRANE PROTEIN /

BauA / outer-membrane transporter

Function / homology

Function and homology information

: / siderophore uptake transmembrane transporter activity / cell outer membrane /

signaling receptor activity / membrane => GO:0016020
Similarity search - Function

Biological species

Acinetobacter baumannii (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.54 Å

Authors

Moynie, L. / Naismith, J.H.

Funding support

United Kingdom, 1items

Citation

Journal: Elife / Year: 2018
Title: Preacinetobactin not acinetobactin is essential for iron uptake by the BauA transporter of the pathogenAcinetobacter baumannii.
Authors: Moynie, L. / Serra, I. / Scorciapino, M.A. / Oueis, E. / Page, M.G. / Ceccarelli, M. / Naismith, J.H.

History

Deposition	Jul 31, 2018	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Oct 10, 2018	Provider: repository / Type: Initial release
Revision 1.1	Jan 16, 2019	Group: Data collection / Database references / Structure summary Category: citation / citation_author ...citation / citation_author / database_PDB_rev / database_PDB_rev_record / entity / pdbx_database_proc Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _entity.formula_weight

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6h7v.cif.gz	770.5 KB	Display	PDBx/mmCIF format
PDB format	pdb6h7v.ent.gz	663.6 KB	Display	PDB format
PDBx/mmJSON format	6h7v.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/h7/6h7v ftp://data.pdbj.org/pub/pdb/validation_reports/h7/6h7v	HTTPS FTP

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Related structure data

Related structure data	6h7fC 6hcpC C: citing same article (ref.)
Similar structure data	3qlb-2 3qlb-1 6bug-3 6buh-2 6bug-2 6bug-1 6i98-d 6dxp-d 1qkc-d 1qjq-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

6h7fC

6hcpC

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Ligand-gated channel protein

B: Ligand-gated channel protein

C: Ligand-gated channel protein

hetero molecules

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

1

A: Ligand-gated channel protein

hetero molecules

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

2

B: Ligand-gated channel protein

hetero molecules

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

3

C: Ligand-gated channel protein

hetero molecules

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

Unit cell

Length a, b, c (Å)	182.310, 220.420, 101.670
Angle α, β, γ (deg.)	90.00, 98.65, 90.00
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
1	2	A
2	2	C
1	3	B
2	3	C

NCS domain segments:

Dom-ID	Ens-ID	Auth asym-ID	Auth seq-ID
1	1	A	33 - 702
2	1	B	33 - 702
1	2	A	33 - 702
2	2	C	33 - 702
1	3	B	33 - 703
2	3	C	33 - 703

NCS ensembles :

ID
1
2
3

#1: Protein	Ligand-gated channel protein / Ligand-gated ion channel / TonB-dependent siderophore receptor Mass: 76892.383 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / CIP 70.34 / JCM 6841 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81) (bacteria) Strain: ATCC 19606 / DSM 30007 / CIP 70.34 / JCM 6841 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81 Gene: BIT33_06105, HMPREF0010_02301 / Production host: Escherichia coli (E. coli) / References: UniProt: D0CC21
#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Chemical	ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE Mass: 306.438 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C₁₆H₃₄O₅ / Comment: C8E, detergent*YM
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 303 / 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: 4.59 Å³/Da / Density % sol: 73.22 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 8000, Hepes, KCl, ethylene glycol

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97957 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 29, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97957 Å / Relative weight: 1
Reflection	Resolution: 2.54→139.53 Å / Num. obs: 130065 / % possible obs: 99.9 % / Redundancy: 15.2 % / R_merge(I) obs: 0.12 / Net I/σ(I): 19.3
Reflection shell	Resolution: 2.54→2.61 Å / Redundancy: 14.1 % / R_merge(I) obs: 0.789 / Mean I/σ(I) obs: 3.8 / Num. unique obs: 9607 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0218	refinement
XDS		data reduction
XSCALE		data scaling
Auto-Rickshaw		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.54→139.53 Å / Cor.coef. F_o:F_c: 0.942 / Cor.coef. F_o:F_c free: 0.923 / SU B: 12.638 / SU ML: 0.135 / Cross valid method: THROUGHOUT / ESU R: 0.244 / ESU R Free: 0.198 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.21295	6485	5 %	RANDOM
R_work	0.18336	-	-	-
obs	0.18483	123580	99.93 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 43.41 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.25 Å²	0 Å²	1.26 Å²
2-	-	-0.5 Å²	0 Å²
3-	-	-	-0.13 Å²

Refinement step

Cycle: 1 / Resolution: 2.54→139.53 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	15416	0	202	303	15921

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.02	15974
X-RAY DIFFRACTION	r_bond_other_d	0	0.02	14385
X-RAY DIFFRACTION	r_angle_refined_deg	1.239	1.964	21654
X-RAY DIFFRACTION	r_angle_other_deg	0.622	3	33525
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.671	5	2013
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.784	24.706	697
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.675	15	2364
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	21.821	15	63
X-RAY DIFFRACTION	r_chiral_restr	0.085	0.2	2367
X-RAY DIFFRACTION	r_gen_planes_refined	0.014	0.021	17929
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	3210
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
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
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
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	1.569	1.995	8058
X-RAY DIFFRACTION	r_mcbond_other	1.569	1.995	8057
X-RAY DIFFRACTION	r_mcangle_it	2.47	2.99	10069
X-RAY DIFFRACTION	r_mcangle_other	2.47	2.99	10070
X-RAY DIFFRACTION	r_scbond_it	2.758	2.383	7916
X-RAY DIFFRACTION	r_scbond_other	2.758	2.383	7917
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	4.058	3.412	11586
X-RAY DIFFRACTION	r_long_range_B_refined	5.496	23.592	16048
X-RAY DIFFRACTION	r_long_range_B_other	5.492	23.518	16003
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	20823	0.07
1	2	B	20823	0.07
2	1	A	20729	0.08
2	2	C	20729	0.08
3	1	B	20726	0.08
3	2	C	20726	0.08

LS refinement shell

Resolution: 2.54→2.606 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.285	506	-
R_work	0.267	9099	-
obs	-	-	99.97 %

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	0.9205	0.3003	-0.0698	4.472	-0.0422	0.6543	0.0149	-0.1608	0.0271	0.034	-0.1799	-0.5511	0.0141	0.2153	0.165	0.2323	-0.0194	0.0038	0.2589	0.0753	0.2959	49.7175	102.0912	13.4696
2	3.1538	1.2123	-0.8424	0.5178	-0.4084	0.45	-0.0828	0.0571	-0.104	-0.0286	-0.0346	-0.132	-0.0326	0.1619	0.1174	0.2562	-0.0285	0.003	0.1483	0.0364	0.213	37.373	103.5928	8.6089
3	0.3979	-0.6784	-0.3354	1.8307	-0.0172	0.9647	0.0787	0.0504	-0.0112	-0.2048	-0.1931	-0.2659	0.0413	0.1617	0.1144	0.2833	0.0626	0.078	0.2017	0.0172	0.3136	44.6163	91.961	-2.608
4	2.2898	1.0548	-1.1086	1.8088	-0.6066	0.988	-0.047	-0.0718	-0.0714	-0.1825	-0.0649	-0.1006	0.0265	0.2015	0.1119	0.2088	-0.0074	-0.0106	0.0646	0.0263	0.1392	26.5659	99.3992	3.5905
5	9.5507	6.2355	3.6685	5.2163	2.5515	2.1917	0.0477	0.0615	0.0249	0.0227	0.0128	-0.2069	-0.0463	0.1536	-0.0605	0.3018	0.0162	0.0473	0.1244	0.0556	0.2334	41.2514	117.4119	0.1831
6	2.5997	1.6378	-0.0392	2.6772	-0.5044	0.7846	-0.1235	0.1576	0.3065	-0.1505	0.1489	0.1713	-0.0808	0.0301	-0.0254	0.1731	-0.0018	0.0737	0.022	0.0107	0.1169	26.0964	107.8216	3.7905
7	2.3726	-0.098	1.3789	2.017	-0.98	3.1104	0.013	-0.27	0.3611	0.1512	0.0197	0.1184	-0.3227	-0.242	-0.0327	0.2851	-0.0593	0.0345	0.0909	-0.0496	0.2348	31.3262	119.4923	16.9031
8	6.2197	-3.3566	-0.1635	3.4881	0.0629	0.931	0.0726	-0.2595	0.2037	0.1217	-0.0988	-0.2993	-0.0276	0.1821	0.0262	0.2756	-0.0828	0.0004	0.2465	0.0747	0.1617	38.2608	99.6954	25.406
9	2.3423	-0.3468	-0.1041	1.0745	-0.2112	0.6185	0.0538	-0.11	-0.1564	-0.0354	-0.0532	-0.2297	-0.0145	0.1781	-0.0006	0.2079	-0.0188	0.0141	0.0808	0.0616	0.1991	35.7717	87.3641	16.9274
10	1.1754	-0.1458	-0.3242	1.9334	-2.5134	3.9709	-0.0159	-0.0479	-0.1155	0.0576	-0.175	-0.2892	-0.1691	0.5024	0.1909	0.2297	-0.0254	0.0046	0.2815	-0.0391	0.2221	56.4693	65.8728	-46.9823
11	2.5573	0.0946	1.9845	0.0744	0.1014	1.5966	-0.1554	0.0445	0.1382	0.0861	0.0659	-0.04	-0.1566	0.1345	0.0896	0.309	-0.0129	0.0347	0.1894	-0.006	0.1641	44.1633	70.2871	-46.1248
12	0.911	0.6849	-0.5671	0.926	-0.0864	1.3565	0.0935	-0.0741	0.259	0.0938	-0.0673	0.008	-0.242	0.3596	-0.0262	0.3119	-0.1406	0.0063	0.2335	0.0598	0.3182	53.3418	85.2887	-48.6207
13	1.5612	0.1808	1.074	0.6449	-0.0263	2.747	-0.0574	0.0357	0.0508	0.0823	0.0775	-0.0663	-0.337	0.139	-0.0201	0.2247	0.0022	0.0577	0.0639	0.0232	0.1433	34.4255	77.4883	-49.6887
14	7.9673	-6.6528	4.359	6.7561	-4.3501	3.1713	0.2029	0.1719	0.2188	-0.057	-0.2722	-0.157	0.0214	0.1838	0.0693	0.2887	-0.0148	0.0695	0.2312	-0.0024	0.1083	43.6165	70.6851	-30.1364
15	1.254	-0.5701	0.2562	0.6811	-0.3575	3.0705	-0.1249	-0.2687	0.0252	0.1541	0.1812	0.0407	-0.3812	-0.355	-0.0562	0.1959	0.0037	0.0208	0.1231	0.0109	0.135	32.5133	73.0703	-42.93
16	2.3697	-0.3215	-1.3176	0.628	0.137	2.1765	0.0312	0.0458	-0.1388	-0.0262	-0.0493	0.0241	0.0965	-0.0776	0.0181	0.2292	-0.0051	-0.0108	0.0934	0.0559	0.1673	36.5033	55.8211	-39.7143
17	12.5527	3.9804	-4.0081	2.4171	-1.7595	2.3084	0.0157	-0.2335	-0.393	-0.0489	-0.1215	-0.2296	0.0768	0.2732	0.1058	0.2729	0.0171	-0.0173	0.1886	-0.0422	0.1344	45.2012	58.1995	-57.8727
18	2.5158	0.7057	-0.3604	0.8665	-0.3839	1.1533	0.0803	0.0339	0.0501	0.0062	-0.0719	-0.1156	-0.0514	0.2367	-0.0084	0.2209	-0.0241	0.039	0.1208	0.0205	0.1154	46.8885	71.2995	-64.1933
19	2.0573	-0.7232	-1.0634	1.6982	2.0969	5.2092	0.0659	0.0356	0.0375	0.1477	0.0816	-0.2369	0.025	0.4451	-0.1474	0.237	0.0374	-0.0087	0.0872	0.0795	0.2518	45.4071	49.5739	2.6796
20	2.5167	-1.6083	-0.2581	1.2865	-0.0146	0.1834	-0.1297	-0.1712	-0.182	0.1089	0.0587	-0.0261	0.0432	0.0763	0.0711	0.2673	0.0153	-0.0134	0.05	0.0029	0.1783	32.4535	47.2253	2.3544
21	0.2251	-0.2551	0.149	2.5624	1.0171	1.7052	-0.0038	-0.2024	-0.1162	0.2066	0.2016	-0.1609	0.1564	0.1455	-0.1979	0.3331	0.0349	-0.0556	0.2711	0.1086	0.1934	38.8005	40.5372	18.9416
22	1.0396	-1.0424	-0.3095	1.7825	0.4141	0.865	-0.0366	-0.0286	-0.0142	0.1804	0.0481	-0.1042	0.137	-0.0334	-0.0115	0.2593	-0.0085	0.0004	0.0203	0.008	0.129	21.9327	45.2743	5.3216
23	6.0975	0.5093	-3.2485	1.986	0.0515	2.7521	-0.3571	-0.0086	-0.7531	-0.0843	-0.0757	0.0535	0.3145	0.1501	0.4329	0.2104	0.0527	-0.0244	0.0334	-0.0125	0.1266	27.4484	38.5249	-2.9562
24	1.0797	0.0326	-0.2276	1.0173	-0.4263	1.4913	0.0041	0.1605	-0.0931	-0.1188	0.0197	0.065	0.153	0.0135	-0.0239	0.2322	0.0737	0.0295	0.0568	0.0009	0.1197	29.674	47.2061	-14.8213
25	13.6989	1.5257	9.6166	1.2112	1.364	9.0319	-0.0616	0.5345	0.2161	0.0165	0.0097	-0.1385	-0.1642	0.5073	0.052	0.267	0.016	0.0663	0.0402	0.0456	0.2056	32.0607	63.0699	-5.7802
26	21.3606	4.0431	18.6458	12.3793	-4.528	47.2192	-0.7881	-0.3693	0.3472	0.1781	0.1291	-0.8695	-1.213	0.7843	0.659	0.4306	-0.0651	-0.0371	0.2721	-0.0252	0.5203	55.2023	65.1399	21.155
27	2.1672	-0.1312	1.1911	0.5523	-0.057	1.8792	0.1226	-0.056	-0.0973	0.1284	-0.0139	-0.0855	0.0397	0.2222	-0.1087	0.2746	0.0149	0.0167	0.0583	-0.0044	0.1203	33.0809	62.2657	12.7042

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	34 - 78
2	X-RAY DIFFRACTION	2	A	79 - 168
3	X-RAY DIFFRACTION	3	A	169 - 255
4	X-RAY DIFFRACTION	4	A	256 - 342
5	X-RAY DIFFRACTION	5	A	343 - 381
6	X-RAY DIFFRACTION	6	A	382 - 454
7	X-RAY DIFFRACTION	7	A	455 - 561
8	X-RAY DIFFRACTION	8	A	562 - 620
9	X-RAY DIFFRACTION	9	A	621 - 703
10	X-RAY DIFFRACTION	10	B	35 - 78
11	X-RAY DIFFRACTION	11	B	79 - 168
12	X-RAY DIFFRACTION	12	B	169 - 255
13	X-RAY DIFFRACTION	13	B	256 - 342
14	X-RAY DIFFRACTION	14	B	343 - 382
15	X-RAY DIFFRACTION	15	B	383 - 453
16	X-RAY DIFFRACTION	16	B	454 - 570
17	X-RAY DIFFRACTION	17	B	571 - 620
18	X-RAY DIFFRACTION	18	B	621 - 703
19	X-RAY DIFFRACTION	19	C	35 - 78
20	X-RAY DIFFRACTION	20	C	79 - 168
21	X-RAY DIFFRACTION	21	C	169 - 247
22	X-RAY DIFFRACTION	22	C	248 - 401
23	X-RAY DIFFRACTION	23	C	402 - 435
24	X-RAY DIFFRACTION	24	C	436 - 570
25	X-RAY DIFFRACTION	25	C	571 - 613
26	X-RAY DIFFRACTION	26	C	614 - 620
27	X-RAY DIFFRACTION	27	C	621 - 703

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