PDB-6qgw: Crystal structure of E.coli BamA beta-barrel in complex with nano...

ID or keywords:

Entry

Database: PDB / ID: 6qgw

Title

Crystal structure of E.coli BamA beta-barrel in complex with nanobody E6

Components

NanoE6
Outer membrane protein assembly factor BamA

Keywords

MEMBRANE PROTEIN / Beta-Barrel / outer membrane / protein insertion / protein folding / protein maturation

Function / homology

Function and homology information

Bam protein complex / Gram-negative-bacterium-type cell outer membrane assembly / protein insertion into membrane
Similarity search - Function

Biological species

Escherichia coli O157:H7 (bacteria)

Lama glama (llama)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.938 Å

Authors

Hartmann, J.-B. / Kaur, H. / Jakob, R.P. / Zahn, M. / Zimmermann, I. / Seeger, M. / Maier, T. / Hiller, S.

Citation

Journal: J.Biomol.Nmr / Year: 2019
Title: Identification of conformation-selective nanobodies against the membrane protein insertase BamA by an integrated structural biology approach.
Authors: Kaur, H. / Hartmann, J.B. / Jakob, R.P. / Zahn, M. / Zimmermann, I. / Maier, T. / Seeger, M.A. / Hiller, S.

History

Deposition	Jan 14, 2019	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jun 26, 2019	Provider: repository / Type: Initial release
Revision 1.1	Aug 21, 2019	Group: Data collection / Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0	Nov 20, 2019	Group: Atomic model / Database references / Category: atom_site / struct_ref_seq_dif Item: _atom_site.auth_atom_id / _atom_site.label_atom_id / _struct_ref_seq_dif.details
Revision 2.1	Jan 24, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6qgw.cif.gz	301.2 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	6qgw_validation.pdf.gz	2.6 MB	Display	wwPDB validaton report
Full document	6qgw_full_validation.pdf.gz	2.6 MB	Display
Data in XML	6qgw_validation.xml.gz	22.6 KB	Display
Data in CIF	6qgw_validation.cif.gz	32.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qg/6qgw ftp://data.pdbj.org/pub/pdb/validation_reports/qg/6qgw	HTTPS FTP

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Related structure data

Related structure data	6qgxC 6qgyC 4n75S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	2811 6ik5-1 5tqo-1 3e77-1 4ccd-d 7cso-1 4hsa-1 5nan-2 7cso-2 1fgm-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	#21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1)

Deposited unit

A: Outer membrane protein assembly factor BamA

B: NanoE6

hetero molecules

64 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	56.406, 135.542, 89.754
Angle α, β, γ (deg.)	90.00, 102.92, 90.00
Int Tables number	5
Space group name H-M	I121

Components on special symmetry positions

ID	Model	Components
1	1	A-1149- HOH

#1: Protein	Outer membrane protein assembly factor BamA Mass: 46022.789 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Gene: bamA, yaeT, Z0188, ECs0179 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0A942
#2: Antibody	NanoE6 Mass: 13401.981 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli BL21(DE3) (bacteria)
#3: Chemical	ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE Mass: 306.438 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C₁₆H₃₄O₅ / Comment: C8E, detergent*YM
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 289 / 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: 2.81 Å³/Da / Density % sol: 56.29 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 25% PEG 4000, 0.2 M MgCl2, 0.1 M Tris pH 8.5

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99998 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 2, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.99998 Å / Relative weight: 1
Reflection	Resolution: 1.938→43.741 Å / Num. obs: 47131 / % possible obs: 97.1 % / Redundancy: 5.9 % / CC_1/2: 0.995 / R_merge(I) obs: 0.116 / R_pim(I) all: 0.081 / Net I/σ(I): 6.6
Reflection shell	Resolution: 1.938→1.98 Å / Redundancy: 6 % / R_merge(I) obs: 0.996 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 3001 / CC_1/2: 0.556 / R_pim(I) all: 0.673 / % possible all: 92.6

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Processing

Software

Name	Version	Classification
PHENIX	(1.13_2998: ???)	refinement
XDS		data reduction
Aimless		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4n75

4n75

Resolution: 1.938→43.741 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 27.31

	R_factor	Num. reflection	% reflection
R_free	0.2301	2331	4.95 %
R_work	0.189	-	-
obs	0.1911	47131	96.87 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 1.938→43.741 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3810	0	140	298	4248

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	4041
X-RAY DIFFRACTION	f_angle_d	0.82	5427
X-RAY DIFFRACTION	f_dihedral_angle_d	17.079	2337
X-RAY DIFFRACTION	f_chiral_restr	0.054	538
X-RAY DIFFRACTION	f_plane_restr	0.005	700

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 (%)
1.9376-1.9771	0.3345	134	0.3094	2470	X-RAY DIFFRACTION	92
1.9771-2.0201	0.3163	124	0.287	2647	X-RAY DIFFRACTION	97
2.0201-2.0671	0.3238	147	0.2688	2640	X-RAY DIFFRACTION	97
2.0671-2.1188	0.2831	139	0.2614	2610	X-RAY DIFFRACTION	97
2.1188-2.1761	0.2878	148	0.2546	2668	X-RAY DIFFRACTION	97
2.1761-2.2401	0.3169	130	0.2469	2612	X-RAY DIFFRACTION	97
2.2401-2.3124	0.2743	137	0.2512	2631	X-RAY DIFFRACTION	98
2.3124-2.3951	0.2956	117	0.2508	2639	X-RAY DIFFRACTION	96
2.3951-2.491	0.2246	124	0.2205	2566	X-RAY DIFFRACTION	93
2.491-2.6043	0.2293	142	0.1881	2657	X-RAY DIFFRACTION	98
2.6043-2.7416	0.2475	144	0.1919	2658	X-RAY DIFFRACTION	98
2.7416-2.9133	0.2276	144	0.191	2675	X-RAY DIFFRACTION	98
2.9133-3.1382	0.2274	127	0.1855	2727	X-RAY DIFFRACTION	99
3.1382-3.4539	0.2342	144	0.1805	2628	X-RAY DIFFRACTION	97
3.4539-3.9534	0.1874	143	0.1568	2614	X-RAY DIFFRACTION	96
3.9534-4.9798	0.1908	155	0.1386	2683	X-RAY DIFFRACTION	99
4.9798-43.7519	0.232	132	0.1893	2675	X-RAY DIFFRACTION	96

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	0.1834	0.174	0.1323	0.3915	1.2091	0.1336	0.2594	0.0227	-0.5959	0.359	0.0856	-0.374	0.3658	0.0712	0.0106	0.4663	-0.0514	-0.0319	0.347	0.1439	0.4416	-31.3319	-14.0001	31.9944
2	0.8827	0.4792	-0.2398	0.108	-0.21	0.9997	-0.0132	-0.0366	-0.286	0.2066	0.0977	-0.3729	0.2277	0.0369	-0.0002	0.3204	-0.0028	-0.0042	0.2769	0.0433	0.3738	-32.1009	-7.3497	22.9074
3	1.8522	0.7007	0.0134	-0.2745	-0.053	0.1397	-0.0562	-0.0338	-0.0865	0.066	0.0516	0.1014	0.0627	-0.0335	0	0.2839	-0.0069	0.0192	0.2523	-0.0016	0.1917	-26.7814	-0.2057	15.6237
4	0.34	-0.4892	-0.4845	0.0848	0.2558	0.412	0.0657	0.1818	-0.4596	0.0118	-0.022	0.2549	0.017	-0.0039	-0.0002	0.2988	-0.001	-0.0395	0.2668	-0.0103	0.3523	-20.3694	-5.8796	11.0853
5	0.4957	-0.0947	-0.3222	-0.0582	-0.0303	0.3883	-0.0227	0.1243	-0.4167	0.005	0.0466	0.1849	0.1535	0.2729	0.0001	0.4032	0.0673	-0.0136	0.3343	0.0094	0.3604	-5.4795	-13.255	18.5101
6	1.1534	-0.4369	0.062	0.841	-0.4697	0.8632	-0.0428	-0.1649	0.2427	0.1109	0.0252	-0.1427	0.0081	-0.006	0.001	0.267	-0.0066	-0.0112	0.2979	-0.031	0.2651	-12.5916	4.125	23.1896
7	0.488	-0.2396	-0.2693	0.7645	0.8417	0.351	-0.1378	0.1064	0.2405	-0.2077	0.0413	-0.3529	0.1127	0.0415	-0.0139	0.1996	-0.012	-0.0126	0.3029	0.0141	0.3574	-7.3048	5.6713	17.9046
8	1.0498	0.0127	0.1578	-0.0031	0.2222	1.0821	-0.1203	-0.0387	0.246	0.2586	0.0808	0.0862	-0.0525	0.0935	0.0098	0.3341	0.0711	0.0121	0.3326	0.0054	0.2878	-6.4768	-3.2025	32.015
9	0.0045	-0.0255	-0.0278	0.0173	-0.0403	0.036	-0.3485	-0.0385	0.3778	0.1291	-0.1934	-0.1216	-0.1742	-0.2623	0.0001	0.3578	0.0032	-0.0779	0.4371	0.0404	0.4994	-55.0132	28.0736	9.7686
10	-0.028	-0.1045	-0.0627	0.2485	-0.0018	0.0588	0.0749	-0.16	0.3682	-0.2135	-0.2187	0.2108	0.0665	0.2154	-0.0016	0.3156	-0.0635	0.032	0.4034	-0.0678	0.3416	-57.453	19.3831	24.9115
11	0.0347	0.0016	-0.0225	0.0244	-0.0458	0.0483	-0.0213	0.7324	-0.3025	-1.4945	0.244	0.7148	-0.9971	-0.2689	0.0002	0.4997	0.0102	-0.0618	0.5285	0.0382	0.4913	-47.6319	23.883	3.4012
12	0.0619	0.0736	-0.0934	0.0836	-0.1034	0.1018	0.2097	0.0956	0.27	-0.091	-0.0232	-0.2342	-0.0152	-0.0493	0.0001	0.2676	0.0173	0.0035	0.3457	0.0047	0.3884	-47.7425	27.7412	19.5955
13	0.0347	-0.1096	0.0062	0.192	-0.0058	0.037	0.2275	-0.2573	0.1809	-0.0176	-0.2831	0.1552	-0.4237	-0.0978	0.0001	0.3247	0.0153	0.031	0.3353	-0.0668	0.3788	-46.7607	30.6882	24.5175
14	0.1179	-0.1208	-0.0324	0.444	-0.1967	0.1772	0.1	0.0412	0.4185	0.0317	-0.0767	-0.3984	0.5264	-0.2314	-0.0223	0.1878	0.0225	-0.0221	0.3225	-0.0032	0.2984	-38.7313	18.8933	14.5154
15	0.6691	-0.4936	-0.2742	0.4772	0.0697	0.211	0.0899	-0.0214	-0.273	0.039	0.0601	-0.1459	0.5136	-0.0398	-0.0007	0.2731	-0.0379	-0.0249	0.3297	-0.0609	0.3435	-46.3606	18.7037	19.8576
16	0.2298	0.3651	-0.008	0.5909	-0.0599	0.2577	-0.0067	-0.0104	0.2038	0.1567	-0.0998	-0.0045	-0.0523	-0.3272	0.0002	0.2814	-0.0223	0.007	0.3476	-0.0365	0.3088	-51.53	23.3788	24.3216
17	0.4121	-0.1438	-0.0921	0.2208	-0.2628	0.6283	0.033	-0.1981	1.0471	-0.0287	-0.5017	-0.591	-0.0988	0.2923	-0.0204	0.3091	-0.0636	0.0204	0.2761	-0.083	0.596	-39.0413	30.4801	14.8335
18	0.3389	-0.1993	0.2063	0.2413	0.1065	0.2097	0.3209	0.1793	0.6723	0.1526	-0.0158	0.7253	-0.3481	-0.4416	0.0008	0.3327	-0.0017	0.0393	0.4028	-0.0525	0.5503	-55.3772	29.1086	21.5815

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 426 through 453 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 454 through 504 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 505 through 589 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 590 through 620 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 621 through 640 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 641 through 729 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 730 through 766 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 767 through 807 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 2 through 8 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 9 through 25 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 26 through 33 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 34 through 40 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 41 through 52 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 53 through 61 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 62 through 78 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 79 through 100 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 101 through 110 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 111 through 123 )

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