PDB-6eus: Crystal structure of the outer membrane channel DcaP of Acinetoba...

ID or keywords:

Entry

Database: PDB / ID: 6eus

Title

Crystal structure of the outer membrane channel DcaP of Acinetobacter baumannii

Components

DcaP-like protein

Keywords

MEMBRANE PROTEIN / outer membrane protein / Acinetobacter baumannii

Function / homology

Porin, alpha proteobacteria type / Porin subfamily / porin activity / membrane / DcaP

Function and homology information

Biological species

Acinetobacter baumannii (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.2 Å

Authors

Zahn, M. / van den Berg, B.

Citation

Journal: Structure / Year: 2019
Title: A Multidisciplinary Approach toward Identification of Antibiotic Scaffolds for Acinetobacter baumannii.
Authors: Bhamidimarri, S.P. / Zahn, M. / Prajapati, J.D. / Schleberger, C. / Soderholm, S. / Hoover, J. / West, J. / Kleinekathofer, U. / Bumann, D. / Winterhalter, M. / van den Berg, B.

History

Deposition	Oct 31, 2017	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Nov 14, 2018	Provider: repository / Type: Initial release
Revision 1.1	Jun 19, 2019	Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6eus.cif.gz	747.7 KB	Display	PDBx/mmCIF format
PDB format	pdb6eus.ent.gz	647.8 KB	Display	PDB format
PDBx/mmJSON format	6eus.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6eus_validation.pdf.gz	480 KB	Display	wwPDB validaton report
Full document	6eus_full_validation.pdf.gz	503.1 KB	Display
Data in XML	6eus_validation.xml.gz	76.6 KB	Display
Data in CIF	6eus_validation.cif.gz	109 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/eu/6eus ftp://data.pdbj.org/pub/pdb/validation_reports/eu/6eus	HTTPS FTP

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Related structure data

Similar structure data	4d64-d 4kr4-d 6rck-d 5mds-d 5o9c-3 3hw9-1 5o9c-2 5mdp-d 2zld-2 3hwb-2 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

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: DcaP-like protein

B: DcaP-like protein

C: DcaP-like protein

D: DcaP-like protein

E: DcaP-like protein

F: DcaP-like protein

249 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: DcaP-like protein

B: DcaP-like protein

C: DcaP-like protein

defined by author&software
Evidence: gel filtration
125 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

D: DcaP-like protein

E: DcaP-like protein

F: DcaP-like protein

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

Unit cell

Length a, b, c (Å)	107.847, 108.382, 216.202
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Dom-ID	Ens-ID	Auth asym-ID	Auth seq-ID
1	1	A	60 - 405
2	1	B	60 - 405
1	2	A	60 - 405
2	2	C	60 - 405
1	3	A	60 - 405
2	3	D	60 - 405
1	4	A	60 - 405
2	4	E	60 - 405
1	5	A	60 - 405
2	5	F	60 - 405
1	6	B	60 - 405
2	6	C	60 - 405
1	7	B	60 - 405
2	7	D	60 - 405
1	8	B	60 - 405
2	8	E	60 - 405
1	9	B	60 - 405
2	9	F	60 - 405
1	10	C	60 - 405
2	10	D	60 - 405
1	11	C	60 - 405
2	11	E	60 - 405
1	12	C	60 - 405
2	12	F	60 - 405
1	13	D	60 - 405
2	13	E	60 - 405
1	14	D	60 - 405
2	14	F	60 - 405
1	15	E	60 - 405
2	15	F	60 - 405

NCS ensembles :

ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

#1: Protein	DcaP-like protein Mass: 41525.199 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter baumannii (bacteria) Gene: ABUW_0826, B4R90_15245, CAS84_19480, CAT05_14765, CBI29_03066, IX87_10345 Production host: Escherichia coli (E. coli) / References: UniProt: A0A0B9X9I7
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 694 / 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: 2.55 Å³/Da / Density % sol: 51.71 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 8.5% MPD, 8.5% PEG 1000, 8.5% PEG 3350, 0.02 M sodium formate, 0.02 M sodium citrate, 0.02 M sodium oxamate, 0.02 M ammonium acetate, 0.02 M sodium potassium tartrate, 0.05 M MES, 0.05 M imidazole pH 6.5

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97926 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 14, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97926 Å / Relative weight: 1
Reflection	Resolution: 2.2→48.44 Å / Num. obs: 125363 / % possible obs: 97.5 % / Redundancy: 2.9 % / R_merge(I) obs: 0.1 / Net I/σ(I): 6
Reflection shell	Resolution: 2.2→2.24 Å / Redundancy: 3 % / R_merge(I) obs: 0.739 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 6276 / % possible all: 99.1

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0158	refinement
XDS		data reduction
Aimless		data scaling
AutoSol		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.2→108.1 Å / Cor.coef. F_o:F_c: 0.949 / Cor.coef. F_o:F_c free: 0.931 / SU B: 11.474 / SU ML: 0.162 / Cross valid method: THROUGHOUT / ESU R: 0.242 / ESU R Free: 0.192 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.23362	2362	1.9 %	RANDOM
R_work	0.20001	-	-	-
obs	0.20065	122906	97.13 %	-

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: 38.879 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.08 Å²	0 Å²	0 Å²
2-	-	-0.62 Å²	0 Å²
3-	-	-	0.7 Å²

Refinement step

Cycle: 1 / Resolution: 2.2→108.1 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	15906	0	0	694	16600

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.019	0.02	16230
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	14472
X-RAY DIFFRACTION	r_angle_refined_deg	2.041	1.95	21984
X-RAY DIFFRACTION	r_angle_other_deg	1.063	3	33606
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.957	5	2070
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	39.066	24.646	762
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.366	15	2514
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.337	15	78
X-RAY DIFFRACTION	r_chiral_restr	0.126	0.2	2376
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	18612
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	3426
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	1.45	2.108	8298
X-RAY DIFFRACTION	r_mcbond_other	1.45	2.107	8297
X-RAY DIFFRACTION	r_mcangle_it	2.166	3.156	10362
X-RAY DIFFRACTION	r_mcangle_other	2.166	3.157	10363
X-RAY DIFFRACTION	r_scbond_it	2.18	2.353	7932
X-RAY DIFFRACTION	r_scbond_other	2.18	2.353	7932
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	3.256	3.44	11622
X-RAY DIFFRACTION	r_long_range_B_refined	5.302	24.931	17482
X-RAY DIFFRACTION	r_long_range_B_other	5.274	24.749	17373
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	22372	0.06
1	2	B	22372	0.06
2	1	A	22362	0.07
2	2	C	22362	0.07
3	1	A	22312	0.06
3	2	D	22312	0.06
4	1	A	22328	0.06
4	2	E	22328	0.06
5	1	A	22416	0.05
5	2	F	22416	0.05
6	1	B	22448	0.07
6	2	C	22448	0.07
7	1	B	22632	0.05
7	2	D	22632	0.05
8	1	B	22406	0.06
8	2	E	22406	0.06
9	1	B	22316	0.07
9	2	F	22316	0.07
10	1	C	22446	0.06
10	2	D	22446	0.06
11	1	C	22604	0.06
11	2	E	22604	0.06
12	1	C	22310	0.07
12	2	F	22310	0.07
13	1	D	22464	0.06
13	2	E	22464	0.06
14	1	D	22392	0.06
14	2	F	22392	0.06
15	1	E	22268	0.06
15	2	F	22268	0.06

LS refinement shell

Resolution: 2.2→2.257 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.353	191	-
R_work	0.31	9160	-
obs	-	-	98.9 %

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	1.1416	-0.3258	-0.6352	2.826	1.0775	1.1993	0.0362	0.1706	0.1081	-0.3563	0.0665	0.1126	-0.1647	0.0567	-0.1027	0.0819	-0.01	-0.0994	0.0769	0.0193	0.3011	50.5603	39.3741	130.7016
2	1.1558	0.1015	-0.3461	1.3487	0.0234	0.2882	-0.0586	0.1743	0.069	-0.2351	-0.0379	0.2718	-0.0542	-0.1286	0.0965	0.0968	0.009	-0.1038	0.0698	-0.0129	0.3011	41.6513	32.6705	131.9385
3	2.9266	-0.3657	2.0643	4.587	2.7478	9.5107	-0.1517	-0.1596	0.103	0.6372	-0.1526	0.2553	-0.371	0.1865	0.3043	0.17	-0.0468	0.0034	0.1283	-0.0546	0.2855	37.5328	26.888	154.2263
4	1.5419	0.1556	0.1552	2.0219	0.3582	1.0137	-0.0416	0.086	0.1407	-0.0991	-0.0034	0.3947	-0.0431	-0.2505	0.045	0.0254	0.0216	-0.0493	0.104	-0.0773	0.459	29.724	38.2094	140.9407
5	3.4177	2.0661	-1.3284	1.908	-1.1613	2.1024	-0.1031	0.3848	0.128	-0.3055	0.2017	0.1241	0.0758	-0.1478	-0.0986	0.1168	0.0153	-0.0342	0.0717	-0.0605	0.2715	53.6463	19.153	129.1849
6	1.0868	0.2671	0.22	1.1098	-0.1109	0.4849	-0.0727	0.1705	-0.0999	-0.1481	0.0462	-0.0539	0.0337	0.0708	0.0265	0.0586	-0.0099	-0.0227	0.0651	-0.0719	0.2168	61.8404	15.4311	133.294
7	1.1614	0.1902	-0.2535	2.5311	1.4133	4.8212	-0.0086	0.1215	-0.1099	-0.1691	-0.074	0.0458	-0.019	0.0084	0.0826	0.0453	0.0645	-0.0051	0.12	-0.0302	0.2838	73.558	5.8179	135.4517
8	1.5566	-0.4272	0.1383	1.048	-0.7237	1.4924	0.061	0.0903	-0.303	0.0205	-0.0008	-0.0328	0.3099	0.1604	-0.0601	0.1328	0.0551	0.0028	0.04	-0.0637	0.316	62.6653	0.7285	142.7954
9	1.9024	-0.3233	0.5973	1.616	0.0716	1.014	-0.0319	0.1862	0.0699	-0.2587	0.0462	0.0179	-0.0562	0.066	-0.0143	0.0738	-0.0436	0.0117	0.0877	-0.0302	0.2211	67.5204	35.2994	132.418
10	2.0947	-0.8281	0.0384	1.9154	0.2587	0.7712	0.0054	0.2508	0.0939	-0.2179	-0.0344	-0.0746	-0.2074	0.2022	0.0291	0.1236	-0.0702	0.0046	0.1242	-0.0041	0.2283	72.0144	49.9097	134.2924
11	2.045	0.1578	-1.28	0.9714	-0.5872	3.816	-0.0593	-0.0117	0.0956	-0.1852	0.0005	-0.0324	0.0255	0.3854	0.0588	0.189	-0.075	-0.015	0.1005	-0.0267	0.2527	71.0457	54.3315	140.5295
12	1.7223	-0.7172	-0.5775	1.9016	0.5418	1.5302	0.0221	0.0809	0.1418	-0.1165	0.085	-0.1835	-0.2664	0.3007	-0.1071	0.0915	-0.107	-0.009	0.1539	-0.0265	0.2817	80.3478	48.4684	144.5241
13	2.4208	1.414	1.932	3.2995	2.4958	3.3751	0.0343	-0.2055	-0.0924	0.1652	-0.0513	-0.0093	0.1085	-0.1904	0.017	0.0408	0.0214	0.0433	0.0951	-0.0315	0.2492	-6.3605	81.7522	141.3487
14	1.3358	-0.0463	0.2441	0.9708	-0.3729	0.584	-0.0037	-0.0945	0.0153	0.0947	-0.0333	0.0826	-0.0047	-0.0978	0.037	0.0332	-0.0054	0.0204	0.0698	-0.0721	0.2388	-11.8474	91.728	137.318
15	1.8938	-0.0279	-1.7649	2.6076	-0.5156	6.161	-0.1839	0.123	-0.0463	0.1013	0.0938	0.0122	0.1304	-0.3815	0.0901	0.0434	0.0139	-0.0738	0.0884	-0.0911	0.2877	-20.0391	99.9907	130.7641
16	1.4693	-0.4589	1.2061	1.6373	0.2125	1.3399	-0.0957	-0.1684	-0.1452	0.0293	0.0545	0.1441	-0.1098	-0.3058	0.0412	0.0128	0.0454	-0.0006	0.2518	-0.1457	0.364	-25.2304	89.8005	127.734
17	1.5008	-0.2812	-0.0081	1.5705	-0.4291	0.5777	0.0043	-0.1109	0.012	0.0186	-0.0026	-0.0317	0.0642	-0.0263	-0.0017	0.0222	0.0004	-0.009	0.0453	-0.0883	0.2374	7.9901	96.4167	136.9709
18	1.0892	0.2155	-0.4082	1.4163	-0.148	0.8528	0.023	-0.0857	0.0234	0.1056	-0.0588	-0.1252	0.0377	0.112	0.0359	0.0298	0.01	-0.0282	0.0505	-0.0852	0.2635	24.2259	100.0556	136.3006
19	1.6011	-0.8	-0.0025	1.9122	0.7593	2.5088	0.196	-0.0593	-0.0439	0.0337	-0.0568	-0.2181	0.1069	-0.1257	-0.1393	0.0438	-0.0297	0.0177	0.0556	-0.0459	0.3005	27.7447	100.5332	129.1306
20	1.8351	-0.2977	-0.4374	0.9421	0.2644	1.4352	0.012	0.0128	0.0608	-0.1145	0.0073	-0.0246	-0.1736	0.1081	-0.0194	0.0568	-0.0275	-0.004	0.0381	-0.0613	0.2849	21.7959	109.0132	124.5525
21	1.8909	0.1016	-0.4055	1.1314	0.3363	0.5544	0.0028	-0.1156	-0.128	0.1043	-0.0088	-0.0008	0.0792	0.0615	0.0061	0.0588	0.0349	-0.0516	0.0345	-0.0489	0.2636	10.9025	78.5484	137.8332
22	3.2743	0.0014	-0.6285	0.9437	0.8045	0.9434	-0.1545	-0.2052	-0.318	0.1071	0.0078	0.0648	0.2566	0.0326	0.1466	0.1623	0.0129	0.0206	0.05	-0.0068	0.3269	4.9475	62.8369	137.8463
23	5.5954	-1.8121	-0.9883	3.8707	-1.4615	1.2532	-0.3637	-0.7182	-0.3868	-0.0036	0.0553	-0.1552	0.3248	0.0976	0.3084	0.3857	-0.1666	0.1097	0.2418	-0.0261	0.465	5.3431	55.826	137.7479
24	2.0157	0.432	-0.0361	1.7833	0.3352	1.5237	-0.102	0.091	-0.2906	0.0861	0.0483	0.0249	0.3195	0.0297	0.0537	0.1521	0.0415	0.0484	0.0401	-0.0756	0.4071	15.0259	58.7829	127.7333

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	60 - 96
2	X-RAY DIFFRACTION	2	A	97 - 211
3	X-RAY DIFFRACTION	3	A	212 - 221
4	X-RAY DIFFRACTION	4	A	222 - 365
5	X-RAY DIFFRACTION	5	B	20 - 94
6	X-RAY DIFFRACTION	6	B	95 - 197
7	X-RAY DIFFRACTION	7	B	198 - 244
8	X-RAY DIFFRACTION	8	B	245 - 365
9	X-RAY DIFFRACTION	9	C	60 - 161
10	X-RAY DIFFRACTION	10	C	162 - 215
11	X-RAY DIFFRACTION	11	C	216 - 242
12	X-RAY DIFFRACTION	12	C	243 - 365
13	X-RAY DIFFRACTION	13	D	20 - 94
14	X-RAY DIFFRACTION	14	D	95 - 215
15	X-RAY DIFFRACTION	15	D	216 - 242
16	X-RAY DIFFRACTION	16	D	243 - 365
17	X-RAY DIFFRACTION	17	E	60 - 156
18	X-RAY DIFFRACTION	18	E	157 - 214
19	X-RAY DIFFRACTION	19	E	215 - 244
20	X-RAY DIFFRACTION	20	E	245 - 365
21	X-RAY DIFFRACTION	21	F	60 - 154
22	X-RAY DIFFRACTION	22	F	155 - 221
23	X-RAY DIFFRACTION	23	F	222 - 251
24	X-RAY DIFFRACTION	24	F	252 - 365

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