PDB-5d0o: BamABCDE complex, outer membrane beta barrel assembly machinery e...

ID or keywords:

Entry

Database: PDB / ID: 5d0o

Title

BamABCDE complex, outer membrane beta barrel assembly machinery entire complex

Components

Outer membrane protein assembly factor BamA
Outer membrane protein assembly factor BamB
Outer membrane protein assembly factor BamC
Outer membrane protein assembly factor BamD
Outer membrane protein assembly factor BamE

Keywords

PROTEIN TRANSPORT / E.coli / Bacterial outer membrane beta barrel assembly machinery / outer membrane biogenesis / protein transport.

Function / homology

Function and homology information

Bam protein complex / Gram-negative-bacterium-type cell outer membrane assembly / protein insertion into membrane / cell outer membrane / protein-macromolecule adaptor activity / cell adhesion / response to antibiotic / cell surface / identical protein binding / membrane
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.9 Å

Authors

Gu, Y. / Paterson, N. / Zeng, Y. / Dong, H. / Wang, W. / Dong, C.

Citation

Journal: Nature / Year: 2016
Title: Structural basis of outer membrane protein insertion by the BAM complex.
Authors: Gu, Y. / Li, H. / Dong, H. / Zeng, Y. / Zhang, Z. / Paterson, N.G. / Stansfeld, P.J. / Wang, Z. / Zhang, Y. / Wang, W. / Dong, C.

History

Deposition	Aug 3, 2015	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Mar 9, 2016	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5d0o.cif.gz	826.4 KB	Display	PDBx/mmCIF format
PDB format	pdb5d0o.ent.gz	729.5 KB	Display	PDB format
PDBx/mmJSON format	5d0o.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5d0o_validation.pdf.gz	470.4 KB	Display	wwPDB validaton report
Full document	5d0o_full_validation.pdf.gz	486.2 KB	Display
Data in XML	5d0o_validation.xml.gz	48.9 KB	Display
Data in CIF	5d0o_validation.cif.gz	66 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/d0/5d0o ftp://data.pdbj.org/pub/pdb/validation_reports/d0/5d0o	HTTPS FTP

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Related structure data

Related structure data	5d0qC C: citing same article (ref.)
Similar structure data	5ayw-d 6lyr-d 7nri-d 6lyq-d 7ajp-d 5a34-d 5jj4-d 4ggp-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
Related items in Molecule of the Month	#261 - Sep 2021 DNA-Sequencing Nanopores similarity (1) #22 - Oct 2001 Photosystem I similarity (1) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (1) #29 - May 2002 Penicillin-binding Proteins similarity (1) #95 - Nov 2007 Multidrug Resistance Transporters similarity (1)

Deposited unit

A: Outer membrane protein assembly factor BamA

B: Outer membrane protein assembly factor BamB

C: Outer membrane protein assembly factor BamC

D: Outer membrane protein assembly factor BamD

E: Outer membrane protein assembly factor BamE

211 kDa, 5 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)	116.689, 116.689, 435.192
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	92
Space group name H-M	P4₁2₁2

#1: Protein	Outer membrane protein assembly factor BamA / Omp85 Mass: 90643.383 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: bamA, yaeT, yzzN, yzzY, b0177, JW0172 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A940
#2: Protein	Outer membrane protein assembly factor BamB Mass: 41918.945 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: bamB, yfgL, b2512, JW2496 / Production host: Escherichia coli (E. coli) / References: UniProt: P77774
#3: Protein	Outer membrane protein assembly factor BamC Mass: 36875.277 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: bamC, dapX, nlpB, b2477, JW2462 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A903
#4: Protein	Outer membrane protein assembly factor BamD Mass: 27858.350 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: bamD, yfiO, b2595, JW2577 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AC02
#5: Protein	Outer membrane protein assembly factor BamE Mass: 13530.256 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: bamE, smpA, b2617, JW2598 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A937

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.51 Å³/Da / Density % sol: 64.99 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M HEPES, pH7.5, 30% PEG600, CYMAL-4 / PH range: 7.2-7.8

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Data collection

Diffraction	Mean temperature: 196 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1.8233 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 12, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.8233 Å / Relative weight: 1
Reflection	Resolution: 2.9→49.65 Å / Num. obs: 67553 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1.5 / Redundancy: 26.4 % / R_merge(I) obs: 0.18 / R_sym value: 0.02 / Net I/av σ(I): 1.5 / Net I/σ(I): 15
Reflection shell	Resolution: 2.9→2.97 Å / Redundancy: 15 % / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
XDS		data reduction
SCALA		data scaling
SHELXDE		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.9→49.653 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 39.42 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.3041	3224	4.77 %	0.05
R_work	0.2762	-	-	-
obs	0.2776	67553	99.51 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.9→49.653 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11614	0	0	0	11614

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	11867
X-RAY DIFFRACTION	f_angle_d	0.809	16128
X-RAY DIFFRACTION	f_dihedral_angle_d	15.282	4296
X-RAY DIFFRACTION	f_chiral_restr	0.032	1760
X-RAY DIFFRACTION	f_plane_restr	0.003	2125

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 (%)
2.9-2.9433	0.457	134	0.4655	2750	X-RAY DIFFRACTION	100
2.9433-2.9893	0.532	136	0.4667	2747	X-RAY DIFFRACTION	100
2.9893-3.0383	0.4839	138	0.4356	2719	X-RAY DIFFRACTION	99
3.0383-3.0907	0.4069	126	0.4253	2741	X-RAY DIFFRACTION	99
3.0907-3.1469	0.4152	141	0.3947	2748	X-RAY DIFFRACTION	99
3.1469-3.2074	0.4244	127	0.3614	2726	X-RAY DIFFRACTION	99
3.2074-3.2729	0.3668	126	0.3575	2766	X-RAY DIFFRACTION	100
3.2729-3.344	0.4424	141	0.3468	2775	X-RAY DIFFRACTION	99
3.344-3.4218	0.3387	109	0.321	2764	X-RAY DIFFRACTION	99
3.4218-3.5073	0.3475	157	0.3088	2723	X-RAY DIFFRACTION	99
3.5073-3.6021	0.3145	162	0.3056	2738	X-RAY DIFFRACTION	99
3.6021-3.7081	0.2941	138	0.2921	2746	X-RAY DIFFRACTION	100
3.7081-3.8277	0.301	133	0.2821	2797	X-RAY DIFFRACTION	99
3.8277-3.9645	0.2964	127	0.2755	2791	X-RAY DIFFRACTION	100
3.9645-4.1231	0.3201	145	0.2698	2794	X-RAY DIFFRACTION	100
4.1231-4.3107	0.2653	146	0.2507	2782	X-RAY DIFFRACTION	100
4.3107-4.5378	0.2883	139	0.2318	2798	X-RAY DIFFRACTION	100
4.5378-4.8219	0.274	151	0.2228	2822	X-RAY DIFFRACTION	100
4.8219-5.1938	0.2572	145	0.2231	2839	X-RAY DIFFRACTION	100
5.1938-5.7158	0.2806	157	0.2452	2834	X-RAY DIFFRACTION	100
5.7158-6.5413	0.3112	161	0.2557	2871	X-RAY DIFFRACTION	100
6.5413-8.2353	0.2784	122	0.2614	2957	X-RAY DIFFRACTION	100
8.2353-49.6606	0.2829	163	0.275	3101	X-RAY DIFFRACTION	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	0.4525	0.0147	0.1909	0.6485	0.1535	0.4424	0.2136	-0.1235	0.2543	0.3092	-0.4866	0.5857	-0.7055	-0.3488	-0.0001	1.7512	0.0053	0.263	1.0066	0.0573	1.3423	2.858	39.316	54.8501
2	0.6404	0.2081	-0.1428	0.9433	-0.0522	0.0089	0.1358	-1.1501	-0.5847	0.3333	-0.1961	-0.5466	0.5788	1.187	-0.0004	1.8265	-0.0312	0.0644	1.3607	-0.021	1.3833	22.9973	43.9042	30.975
3	0.659	0.1585	-0.1773	0.5867	0.0601	0.619	0.0238	0.1421	-0.0333	0.278	-0.0464	-0.0731	0.088	0.198	-0	1.4007	0.1917	-0.0475	1.0501	0.0327	1.1728	61.1333	25.2276	20.5594
4	0.3039	0.2774	0.3609	0.6605	0.15	0.4861	-0.4763	0.4944	-0.328	-0.2178	-0.0528	-0.1262	-0.5445	0.1526	0.0002	1.1903	0.1066	0.0101	1.1944	-0.0072	1.3184	72.3183	32.9424	3.7294
5	0.1915	0.3109	0.054	0.3373	0.0514	-0.0043	0.1374	1.6744	0.7389	-0.6828	-0.1144	0.1919	-1.0753	-0.1696	0	1.6786	0.2637	-0.2588	1.2979	0.2275	1.3036	40.9589	82.2183	12.7437
6	1.5913	0.5253	0.1888	0.9521	0.2338	0.6585	-0.0217	0.5016	0.0429	-0.1335	0.3869	-0.3616	-0.4556	0.3498	-0.0001	1.785	0.0748	0.1302	1.0322	0.0961	1.2655	63.5323	76.1265	24.604
7	1.2995	-0.5324	0.3295	1.9452	0.7955	2.1207	0.2264	-0.0076	0.086	-0.1864	-0.302	0.2073	0.1508	-0.3565	-0	1.4045	0.084	0.123	1.0037	0.0014	1.2185	46.0051	76.717	35.0659
8	0.0201	-0.0138	0.0074	0.0091	-0.0021	0.0033	-0.0628	0.8094	0.8197	-0.2937	-0.0985	-0.7817	-0.1304	0.2778	-0.0003	2.2772	0.4639	0.4092	1.4058	-0.0873	1.702	24.0874	16.1593	21.9586
9	0.7307	-0.0645	0.0399	0.3488	-0.0467	-0.0168	0.1416	0.2023	-0.1445	0.3575	-0.4239	0.4294	0.3237	0.7819	0	1.3441	0.037	0.0595	0.9435	-0.135	1.4203	17.6021	2.4893	41.4071
10	0.0053	0.021	0.0123	0.0149	0.0012	0.0238	0.0804	0.2918	-0.0678	0.249	-0.1339	1.4675	-0.2297	-0.3806	-0.0002	2.8116	0.2074	-0.3401	1.2653	0.3391	1.4462	-1.4053	32.5782	18.8712
11	0.0125	0.0099	-0.0089	0.006	-0.0095	0.0269	0.2756	0.4236	-0.2825	-0.0292	-0.0604	0.7951	0.0585	0.1554	0.0001	2.2872	-0.527	-0.4758	1.4588	0.255	1.4002	3.2783	20.3914	17.276
12	0.0417	0.0415	0.007	0.0571	-0.0407	0.0682	-0.2726	0.9056	0.2375	-0.3118	0.4509	-1.2686	-0.4799	0.6474	0.0004	2.0212	0.3525	-0.1226	1.4575	-0.1055	1.3435	7.8614	29.9658	21.6784
13	0.9776	0.1435	-0.0769	0.0955	0.269	1.4212	0.1623	-0.15	-0.0773	-0.3849	-0.0433	0.2126	0.1179	-0.0209	-0.0001	1.7123	-0.0141	0.1379	0.663	-0.0703	1.2541	22.4264	12.104	39.3045
14	0.1056	0.0931	-0.0999	0.1324	-0.1011	0.0885	-0.1959	0.729	-0.481	-0.2016	-0.1597	0.0357	0.9862	-0.0154	0.0015	2.0229	0.164	0.156	0.6799	0.1487	1.2872	37.3052	-10.2261	51.1254
15	0.0601	0.0597	-0.0507	0.0313	-0.0452	0.0369	1.1052	0.1662	-0.741	0.0983	0.1653	-0.8358	0.0097	0.4367	0.0038	1.6995	-0.0063	0.199	0.8834	0.1923	1.3295	55.9152	9.8495	51.149
16	0.2113	0.0598	0.0612	0.0166	0.0165	0.0173	0.0597	-0.0208	-0.0047	0.0391	-0.0986	-0.1014	-0.1029	0.0323	-0.0679	1.5968	-0.6008	0.3537	0.8462	0.5249	2.3261	57.4736	11.0155	68.8882
17	0.3134	-0.1198	0.0932	0.3854	0.0037	0.1344	0.7948	0.0555	0.233	0.6781	-0.0004	0.126	-0.35	0.3482	0.0002	1.8826	0.0541	0.106	1.0174	0.0639	1.2649	46.8524	6.3477	63.5885
18	0.3647	-0.1926	0.2639	0.3114	0.2324	0.8846	0.8704	0.5655	0.3172	1.2988	0.0475	-0.8144	0.1315	0.2591	0.0399	2.0525	-0.1556	0.0187	0.9936	0.0666	1.4167	53.1273	1.1164	61.2234

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 24 through 88 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 89 through 144 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 145 through 766 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 767 through 809 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 31 through 51 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 52 through 125 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 126 through 391 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 30 through 36 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 37 through 85 )
10	X-RAY DIFFRACTION	10	chain 'D' and (resid 27 through 39 )
11	X-RAY DIFFRACTION	11	chain 'D' and (resid 40 through 47 )
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 48 through 61 )
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 62 through 227 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 228 through 244 )
15	X-RAY DIFFRACTION	15	chain 'E' and (resid 29 through 40 )
16	X-RAY DIFFRACTION	16	chain 'E' and (resid 41 through 45 )
17	X-RAY DIFFRACTION	17	chain 'E' and (resid 46 through 80 )
18	X-RAY DIFFRACTION	18	chain 'E' and (resid 81 through 111 )

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