PDB-9co2: Crystal structure of BamA in complex with the PTB2 open-state inh...

ID or keywords:

Entry

Database: PDB / ID: 9co2

Title

Crystal structure of BamA in complex with the PTB2 open-state inhibitor (anisotropic data set)

Components

Outer membrane protein assembly factor BamA
PTB2 circular peptide

Keywords

MEMBRANE PROTEIN / protein crystal structure / circular peptide

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 (E. coli)
synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.75 Å

Authors

Sun, D. / Payandeh, J.

Funding support

1items

Citation

Journal: Nat Commun / Year: 2024
Title: The discovery and structural basis of two distinct state-dependent inhibitors of BamA.
Authors: Dawei Sun / Kelly M Storek / Dimitry Tegunov / Ying Yang / Christopher P Arthur / Matthew Johnson / John G Quinn / Weijing Liu / Guanghui Han / Hany S Girgis / Mary Kate Alexander / Austin K ...
Abstract: BamA is the central component of the essential β-barrel assembly machine (BAM), a conserved multi-subunit complex that dynamically inserts and folds β-barrel proteins into the outer membrane of ...

History

Deposition	Jul 16, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 15, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9co2.cif.gz	635.2 KB	Display	PDBx/mmCIF format
PDB format	pdb9co2.ent.gz	531.8 KB	Display	PDB format
PDBx/mmJSON format	9co2.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9co2_validation.pdf.gz	496.5 KB	Display	wwPDB validaton report
Full document	9co2_full_validation.pdf.gz	551.7 KB	Display
Data in XML	9co2_validation.xml.gz	61.8 KB	Display
Data in CIF	9co2_validation.cif.gz	78.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/co/9co2 ftp://data.pdbj.org/pub/pdb/validation_reports/co/9co2	HTTPS FTP

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Related structure data

Related structure data	45764C 45765C 45766C 45767C 45768C 9cnwC 9cnxC 9cnyC 9cnzC 9co0C C: citing same article (ref.)
Similar structure data	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: Outer membrane protein assembly factor BamA

B: Outer membrane protein assembly factor BamA

C: Outer membrane protein assembly factor BamA

D: Outer membrane protein assembly factor BamA

E: PTB2 circular peptide

F: PTB2 circular peptide

G: PTB2 circular peptide

I: PTB2 circular peptide

179 kDa, 8 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)	98.792, 167.274, 104.821
Angle α, β, γ (deg.)	90.00, 110.99, 90.00
Int Tables number	4
Space group name H-M	P12₁1
Symmetry operation	#1: x,y,z #2: -x,y+1/2,-z

#1: Protein	Outer membrane protein assembly factor BamA Mass: 42665.242 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: bamA, yaeT, EcE24377A_0181 / Production host: Escherichia coli (E. coli) / References: UniProt: A7ZHR7
#2: Protein/peptide	PTB2 circular peptide Mass: 2003.382 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
Has ligand of interest	Y
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 4.46 Å³/Da / Density % sol: 72.4 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 100 mM Tris-HCl, pH 8.0, 100 mM NaCl, 325 mM sodium acetate, and 21% PEG 400

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 15, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9791 Å / Relative weight: 1
Reflection	Resolution: 2.746→97.864 Å / Num. obs: 47779 / % possible obs: 90 % / Redundancy: 3.4 % / B_iso Wilson estimate: 52.94 Å² / CC_1/2: 0.997 / Net I/σ(I): 6
Reflection shell	Resolution: 2.75→3 Å / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2389 / CC_1/2: 0.774

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Processing

Software

Name	Version	Classification
PHENIX	(1.20rc3-4406_final: ???)	refinement
autoPROC		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.75→29.59 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 47.2 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.3683	2407	5.08 %
R_work	0.3357	-	-
obs	0.3373	47349	57.31 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.75→29.59 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12648	0	0	0	12648

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005
X-RAY DIFFRACTION	f_angle_d	0.881
X-RAY DIFFRACTION	f_dihedral_angle_d	15.053	4516
X-RAY DIFFRACTION	f_chiral_restr	0.055	1752
X-RAY DIFFRACTION	f_plane_restr	0.006	2344

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 (%)
2.75-2.8	0.0371	1	0.4977	46	X-RAY DIFFRACTION	1
2.8-2.86	0.4111	15	0.5154	254	X-RAY DIFFRACTION	6
2.86-2.93	0.4639	34	0.4941	732	X-RAY DIFFRACTION	16
2.93-3	0.4906	60	0.4451	1201	X-RAY DIFFRACTION	26
3-3.08	0.5158	80	0.4448	1556	X-RAY DIFFRACTION	34
3.08-3.18	0.4368	90	0.4125	1820	X-RAY DIFFRACTION	40
3.18-3.28	0.4128	107	0.4052	2172	X-RAY DIFFRACTION	47
3.28-3.39	0.4116	129	0.376	2491	X-RAY DIFFRACTION	54
3.39-3.53	0.3804	148	0.3816	2808	X-RAY DIFFRACTION	61
3.53-3.69	0.4121	156	0.3719	3042	X-RAY DIFFRACTION	66
3.69-3.88	0.3502	178	0.3384	3350	X-RAY DIFFRACTION	72
3.88-4.13	0.368	212	0.3459	3581	X-RAY DIFFRACTION	78
4.13-4.45	0.3344	224	0.3283	4025	X-RAY DIFFRACTION	88
4.45-4.89	0.3465	250	0.2943	4373	X-RAY DIFFRACTION	95
4.89-5.59	0.3957	220	0.3106	4584	X-RAY DIFFRACTION	98
5.6-7.03	0.3562	243	0.3301	4517	X-RAY DIFFRACTION	97
7.03-29.59	0.3364	260	0.3009	4390	X-RAY DIFFRACTION	94

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	1.9462	-0.8642	0.0457	0.6521	0.6021	1.4296	-0.2079	0.2781	-0.5663	-0.5508	0.1203	-0.5465	0.543	0.2101	0.2607	0.498	0.0525	0.2734	0.5651	-0.1779	0.7813	5.1292	-12.6167	-28.6416
2	0.8194	0.1088	0.1719	0.927	0.1505	1.1707	-0.0173	-0.0904	-0.1582	-0.1565	0.2446	-0.219	0.4544	0.015	-0.0545	0.2974	-0.02	-0.0747	0.2221	-0.1033	0.245	-9.5098	-2.3898	-27.655
3	0.3797	0.1013	0.1687	0.7164	0.2461	0.8262	0.084	0.0579	-0.138	-0.2455	0.2255	-0.3208	0.0333	0.3595	-0.083	0.3592	-0.4345	0.0369	0.1534	-0.2705	0.3677	-10.3552	-1.9348	-45.4692
4	3.6609	-2.0877	-0.7249	6.1956	1.2623	2.7565	0.0896	-0.3814	-0.1676	0.229	0.0073	0.1413	0.0497	-0.135	-0.0068	0.8557	-0.2653	-0.0196	0.9718	0.2584	0.8727	-56.5227	-13.5768	-5.7522
5	2.295	-0.4126	-0.8482	1.1125	0.518	2.1072	0.0272	-0.0239	-0.3048	0.2762	-0.0323	-0.1774	0.4162	-0.0758	-0.0055	0.3656	-0.166	-0.0114	0.2727	-0.0459	0.5958	-47.3689	-11.6374	-14.0231
6	0.8547	-0.0385	0.1505	1.9133	0.4627	1.0695	0.0516	0.1761	-0.1881	0.2038	0.1035	0.3599	0.258	-0.0559	-0.1739	0.2207	-0.0644	0.1255	0.2044	0.0462	0.2419	-37.5628	1.0704	-13.1371
7	0.4024	-0.2577	0.2389	0.248	-0.0355	0.3064	0.1157	-0.1207	-0.3324	0.2261	0.2677	0.2376	0.3534	-0.1346	-0.2594	0.5719	-0.0396	-0.1184	0.1319	-0.006	0.3622	-31.4009	-14.2843	-6.6328
8	0.9717	-0.0401	0.5478	0.491	-0.0438	0.8389	0.2251	0.0264	-0.2444	0.1538	0.2618	-0.1177	0.2881	-0.051	0.2026	0.3178	0.0916	0.0773	0.1629	-0.0742	0.1556	-31.4441	-5.8655	1.5068
9	0.3141	-0.3613	0.2734	0.9879	0.0659	0.4936	0.1414	-0.1745	-0.293	0.3059	0.3631	0.565	0.0857	-0.4287	-0.2163	0.5602	0.138	-0.0922	0.271	0.1863	0.5256	-41.5401	2.9436	7.0482
10	0.5517	-0.555	0.1261	0.639	-0.4504	1.3169	0.0158	-0.0438	-0.1877	0.2545	0.3751	0.5129	0.0984	-0.3365	-0.2595	0.8654	0.1682	0.0495	0.3823	0.1043	0.3271	-34.3721	-1.6916	9.6395
11	1.537	-1.2182	-0.1632	1.0488	0.547	2.0639	0.1909	-0.3187	0.7776	0.3811	0.1777	0.4916	-0.155	-0.176	-0.1417	0.4361	0.2815	0.0235	0.7076	-0.0602	0.821	-24.9409	65.0994	-3.8499
12	0.6112	-0.1797	0.0096	0.1617	-0.0524	0.5892	-0.0889	0.0252	0.3974	-0.0794	0.1527	-0.0159	-0.1217	0.1848	0.4144	0.4515	0.3125	-0.134	0.3142	0.1264	0.2707	-19.6013	61.5811	-21.3905
13	0.369	-0.0465	0.1899	0.8615	-0.4576	0.7227	-0.0543	-0.137	0.0615	0.2022	0.2675	0.4234	-0.1581	-0.1543	-0.075	0.5767	0.2344	0.1042	0.307	0.2762	0.3474	-34.4703	54.0858	-23.7062
14	4.229	-0.1622	-0.0107	3.387	-0.1803	4.863	0.0456	0.231	-0.1129	-0.1957	0.0475	-0.3709	0.3372	0.5635	-0.028	0.7138	-0.3253	-0.0638	1.1878	0.1312	1.1162	18.9597	64.4975	-58.3177
15	1.6493	0.3654	-0.1277	0.3789	-0.7587	2.0644	-0.0148	0.1993	0.5968	-0.2476	0.099	-0.1654	-0.1438	-0.1282	0.0021	0.4064	-0.1335	0.135	0.545	0.0376	0.7187	6.0117	65.0801	-53.2536
16	0.5364	-0.0335	0.2939	0.2024	-0.1068	0.6469	-0.2159	0.0927	0.2757	0.2093	0.229	0.3478	-0.3039	-0.1409	0.082	0.4683	-0.1194	0.1987	0.1812	-0.0732	0.5648	4.2555	61.577	-37.0626
17	0.6215	0.0295	0.2789	1.7118	0.42	1.1752	-0.2135	0.166	-0.3002	0.0637	0.3577	-0.1968	-0.3062	0.0293	-0.0873	0.3915	-0.0337	0.1091	0.2797	-0.1151	0.3436	16.7779	51.327	-34.5525
18	1.712	0.5895	-0.2902	1.4002	0.3939	1.2708	-0.0691	0.2263	0.0416	-0.5219	0.1161	-0.1171	-0.0416	0.0869	-0.1402	0.762	-0.2004	0.0579	0.4812	-0.2653	0.7479	26.3357	62.7988	-35.0596
19	0.103	-0.0187	0.075	0.0032	-0.0145	0.0548	-0.0796	0.0488	0.0745	-0.0675	0.0923	-0.086	-0.0885	0.1242	-0.106	0.4461	-0.2513	0.1378	0.4835	-0.2918	0.3872	3.5766	7.0558	-39.2243
20	0.0026	-0.0061	-0.0048	0.0568	0.0439	0.0341	0.0144	0.0057	0.0276	0.018	-0.0018	0.0416	-0.0155	-0.0429	-0.0302	0.6926	0.016	0.3494	0.73	0.2484	0.608	-51.216	10.6637	0.3536
21	0.0015	-0.0036	0.0019	0.0044	-0.0029	0.002	-0.0765	-0.0669	0.063	0.0471	0.0096	0.0217	-0.0536	-0.0851	0.0002	0.5761	0.0511	0.0052	0.3701	0.1243	0.3653	-47.6533	4.8818	-0.4883
22	0.0027	0.0002	0.0022	0.0035	-0.0017	0.0025	0.0207	-0.0183	0.0133	-0.0068	0.033	0.0349	0.0122	-0.0286	-0	0.8263	0.1284	-0.0318	0.8369	0.1626	0.8552	-35.8772	44.2211	-8.2337
23	0.0002	-0.0007	-0	0.0023	-0.0021	0.0033	-0.0012	0.0054	-0.0196	-0.0172	0.0314	0.0358	0.0062	-0.0139	-0	0.5556	0.0099	-0.0382	0.4725	0.1364	0.4316	-31.1231	51.8905	-11.5381
24	0.0006	0.0003	0.0005	0.0036	0.0021	0.0015	0.0061	0.023	-0.0101	-0.0034	0.0223	-0.0307	0.017	0.022	-0.0001	0.8455	-0.1132	0.1381	0.9263	-0.1055	0.8806	20.5334	44.0253	-50.0675
25	0.0015	-0.0001	0.0014	0.0019	0.0027	0.0041	0.0221	-0.0197	-0.0018	0.0175	0.0298	-0.0244	0.0129	0.0042	-0.0001	0.5719	-0.0519	-0.0876	0.4987	-0.1622	0.4201	15.865	51.8276	-46.958

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 425 through 495 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 496 through 607 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 608 through 806 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 425 through 453 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 454 through 495 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 496 through 581 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 582 through 607 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 608 through 675 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 676 through 734 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 735 through 806 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 425 through 504 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 505 through 640 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 641 through 806 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 425 through 447 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 448 through 504 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 505 through 640 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 641 through 766 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 767 through 806 )
19	X-RAY DIFFRACTION	19	chain 'I' and (resid 2 through 16 )
20	X-RAY DIFFRACTION	20	chain 'E' and (resid 2 through 8 )
21	X-RAY DIFFRACTION	21	chain 'E' and (resid 9 through 16 )
22	X-RAY DIFFRACTION	22	chain 'F' and (resid 2 through 9 )
23	X-RAY DIFFRACTION	23	chain 'F' and (resid 10 through 16 )
24	X-RAY DIFFRACTION	24	chain 'G' and (resid 2 through 9 )
25	X-RAY DIFFRACTION	25	chain 'G' and (resid 10 through 16 )

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