PDB-7xgf: Crystal structure of BCL-xL in complex with computationally desig...

ID or keywords:

Entry

Database: PDB / ID: 7xgf

Title

Crystal structure of BCL-xL in complex with computationally designed inhibitor protein

Components

BCL-xL
BCL-xL and MCL-1 dual inhibitor 2

Keywords

APOTOSIS / DE NOVO PROTEIN / computational design

Biological species

synthetic construct (others)

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.9 Å

Authors

Oh, B.-H. / Kim, S.

Funding support

1items

Citation

Journal: Comput Struct Biotechnol J / Year: 2022
Title: Computational design of an apoptogenic protein that binds BCL-xL and MCL-1 simultaneously and potently.
Authors: Kim, S. / Park, H.S. / Oh, B.H.

History

Deposition	Apr 4, 2022	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jul 20, 2022	Provider: repository / Type: Initial release
Revision 1.1	Apr 3, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7xgf.cif.gz	387.1 KB	Display	PDBx/mmCIF format
PDB format	pdb7xgf.ent.gz	318.5 KB	Display	PDB format
PDBx/mmJSON format	7xgf.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/xg/7xgf ftp://data.pdbj.org/pub/pdb/validation_reports/xg/7xgf	HTTPS FTP

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Related structure data

Related structure data	7xgeC 7xggC C: citing same article (ref.)

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#70 - Oct 2005 Designer Proteins similarity (1)

Deposited unit

A: BCL-xL and MCL-1 dual inhibitor 2

B: BCL-xL

C: BCL-xL

D: BCL-xL and MCL-1 dual inhibitor 2

E: BCL-xL

F: BCL-xL

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

1

A: BCL-xL and MCL-1 dual inhibitor 2

B: BCL-xL

C: BCL-xL

defined by author&software
Evidence: surface plasmon resonance
57.9 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

D: BCL-xL and MCL-1 dual inhibitor 2

E: BCL-xL

F: BCL-xL

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

Unit cell

Length a, b, c (Å)	60.930, 69.050, 79.990
Angle α, β, γ (deg.)	100.790, 110.000, 108.670
Int Tables number	1
Space group name H-M	P1

#1: Protein	BCL-xL and MCL-1 dual inhibitor 2 Mass: 18605.627 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
#2: Protein	BCL-xL Mass: 19639.611 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 502 / 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: 2.44 Å³/Da / Density % sol: 49.59 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 10% PEG 10,0000 (w/v), 0.1M Sodium acetate (pH4.5)

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97959 Å
Detector	Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 27, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97959 Å / Relative weight: 1
Reflection	Resolution: 1.9→29.21 Å / Num. obs: 83355 / % possible obs: 96.4 % / Redundancy: 3.7 % / CC_1/2: 0.998 / Net I/σ(I): 11.9
Reflection shell	Resolution: 1.9→1.96 Å / Num. unique obs: 8334 / CC_1/2: 0.61

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Processing

Software

Name	Version	Classification
XSCALE		data scaling
PHENIX	1.17.1_3660	refinement
PDB_EXTRACT	3.27	data extraction
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: designed model

Resolution: 1.9→29.21 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 21.12 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2061	4166	5 %
R_work	0.1715	79168	-
obs	0.1733	83334	96.65 %

Solvent computation

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

Displacement parameters

B_iso max: 130.3 Å² / B_iso mean: 41.3601 Å² / B_iso min: 12.85 Å²

Refinement step

Cycle: final / Resolution: 1.9→29.21 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7369	0	0	502	7871
B_iso mean	-	-	-	44.98	-
Num. residues	-	-	-	-	918

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 30

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.9-1.92	0.3418	137	0.2903	2601	2738	95
1.92-1.94	0.2554	137	0.2678	2604	2741	96
1.94-1.97	0.2809	139	0.2532	2641	2780	96
1.97-1.99	0.2866	138	0.2543	2627	2765	96
1.99-2.02	0.2847	137	0.2426	2609	2746	96
2.02-2.05	0.2629	138	0.2311	2620	2758	96
2.05-2.08	0.2374	137	0.2151	2601	2738	96
2.08-2.11	0.2303	142	0.1973	2684	2826	96
2.11-2.14	0.2205	135	0.1912	2579	2714	96
2.14-2.17	0.2154	141	0.1816	2681	2822	96
2.17-2.21	0.2154	136	0.185	2581	2717	96
2.21-2.25	0.2264	138	0.177	2616	2754	97
2.25-2.3	0.1973	141	0.1685	2670	2811	96
2.3-2.34	0.1773	139	0.1678	2638	2777	97
2.34-2.39	0.237	137	0.1686	2613	2750	97
2.39-2.45	0.2198	140	0.1733	2664	2804	97
2.45-2.51	0.2022	139	0.1724	2634	2773	96
2.51-2.58	0.2156	140	0.1664	2662	2802	97
2.58-2.65	0.2052	140	0.1713	2667	2807	97
2.65-2.74	0.2059	138	0.1728	2606	2744	97
2.74-2.84	0.182	137	0.1674	2618	2755	96
2.84-2.95	0.2189	140	0.1737	2655	2795	97
2.95-3.09	0.2362	138	0.1783	2621	2759	97
3.09-3.25	0.2189	139	0.1742	2635	2774	97
3.25-3.45	0.1888	139	0.1613	2647	2786	96
3.45-3.72	0.1895	137	0.1593	2592	2729	96
3.72-4.09	0.1797	141	0.1451	2697	2838	98
4.09-4.68	0.1788	142	0.1395	2694	2836	99
4.68-5.89	0.1763	143	0.1714	2710	2853	99
5.89-29.21	0.2165	141	0.1638	2701	2842	99

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	4.4925	1.9469	0.6763	7.5573	0.8657	2.2589	0.0913	0.601	0.0633	-1.1517	0.1231	0.4112	0.0827	0.0353	-0.266	0.2255	0.0622	-0.1087	0.3112	0.0284	0.4242	-16.4668	19.2045	-16.203
2	2.9212	0.2091	-0.2973	4.0343	-0.3423	0.863	0.1557	0.0159	0.0725	-0.2885	-0.184	0.4662	0.0827	-0.0259	0.0416	0.2241	0.0267	-0.0357	0.2634	0.0494	0.2778	-10.4759	12.9525	-11.7994
3	4.8208	1.3337	-0.2795	5.7132	0.2896	1.5736	0.2278	-0.5186	-0.0467	0.6307	-0.2073	0.5719	0.1335	-0.0832	-0.0256	0.2329	0.0575	0.009	0.263	0.0796	0.3811	-17.2464	20.5026	-5.349
4	3.8532	-0.6772	-0.2944	5.142	0.1953	1.8994	0.0415	0.0477	-0.5863	0.1174	0.0337	0.0743	0.2	-0.0705	-0.0306	0.1809	0.0302	-0.0483	0.2165	0.0189	0.2746	-25.0667	23.8403	-11.2423
5	3.9096	0.3463	0.1796	4.1431	0.7214	6.6695	-0.0433	-0.2582	0.25	0.3608	-0.0605	0.3946	-0.0983	-0.5434	0.0316	0.1988	0.0254	-0.0124	0.2085	0.0009	0.2297	-39.4762	40.6888	-12.5411
6	3.1199	0.5264	0.0181	2.2033	-0.0846	2.445	-0.0395	-0.3514	0.2025	0.2557	-0.0987	0.4304	-0.306	-0.5433	0.296	0.294	-0.0094	0.0077	0.3975	-0.0296	0.338	-45.3507	38.8115	-18.8459
7	1.7816	-0.2689	-1.1604	2.0087	0.7638	3.2683	0.0566	0.0391	0.243	-0.0269	-0.0351	-0.0305	-0.4104	-0.0087	0.0001	0.1841	-0.0137	-0.0295	0.1695	0.0166	0.172	-28.7846	42.7075	-15.4891
8	2.5947	0.5456	-0.2487	1.4685	-0.3407	0.5724	-0.0431	0.1614	-0.2769	0.0146	0.006	0.1029	0.1248	-0.1211	0.021	0.198	0.0034	-0.0038	0.1761	-0.0083	0.2105	-31.448	25.1623	-10.8921
9	1.5801	0.3259	0.5221	1.5614	-0.1231	1.423	-0.0057	-0.02	-0.0158	0.1157	-0.0068	-0.0061	-0.0315	-0.1114	0.0246	0.1509	0.007	0.0039	0.1643	-0.0115	0.1626	-36.1229	33.0153	-8.8823
10	4.0683	0.8268	-0.1498	4.387	0.4605	2.4161	0.0676	0.1418	0.3398	-0.6803	-0.0184	-0.5479	-0.4677	0.1061	-0.0259	0.3975	0.0052	0.0111	0.2109	-0.027	0.332	-25.5149	49.4035	-7.6067
11	2.6401	0.3	-0.4793	3.9465	-1.0372	4.2386	0.0947	-0.0561	-0.1118	0.1714	-0.1343	-0.4018	-0.2034	0.5718	0.0139	0.2522	0.0052	-0.026	0.3016	-0.0085	0.2007	6.4296	6.5265	2.2849
12	1.4935	0.7814	0.2179	4.0639	-0.5591	2.7912	0.0508	-0.0408	-0.0024	0.2072	-0.0472	0.3097	0.0675	0.0838	-0.01	0.1804	0.0212	0.0268	0.2077	-0.0251	0.1857	-2.8729	7.6996	-4.29
13	2.0135	1.2579	-0.4164	4.0357	-0.6443	1.7565	0.0109	0.0147	0.0423	-0.0245	-0.0593	-0.1746	0.0776	0.2448	0.0627	0.1694	0.0247	0.0006	0.2402	-0.007	0.1715	4.7701	8.6795	-8.216
14	6.7467	-1.0646	-0.0662	3.8865	0.3001	1.7294	-0.1503	-0.4845	0.3195	0.6564	0.2687	-0.1907	0.1406	-0.0227	-0.0638	0.3135	-0.0288	-0.008	0.2388	-0.0611	0.3043	-33.1968	13.6129	-36.875
15	3.3505	-0.0018	-0.2624	3.4674	0.2048	1.3397	0.1075	0.0915	-0.0199	0.3486	-0.0623	-0.0655	0.1769	0.0192	-0.0121	0.2662	-0.0134	0.0197	0.2119	-0.0517	0.2247	-36.3215	6.4705	-41.4778
16	6.6211	-1.3624	0.5036	3.7719	-0.7716	1.9563	0.2298	0.6089	-0.1527	-0.6856	-0.1382	-0.1205	0.1011	0.1405	-0.1167	0.3088	-0.008	0.0291	0.2186	-0.0397	0.2898	-33.4082	14.9691	-48.5464
17	0.1521	-0.3026	0.6866	1.1914	-2.1264	4.115	-0.1569	-0.316	0.0455	0.2618	-0.2571	-0.2646	0.1826	0.1625	0.2306	0.8094	0.0628	0.0728	1.6235	-0.1679	1.4672	-4.6927	6.2986	-43.6784
18	5.2078	-0.3307	0.1131	4.9499	-0.6369	1.8662	-0.1634	0.0003	-0.3187	0.0787	0.0078	-0.39	-0.054	0.1535	0.0807	0.2122	-0.0439	0.0253	0.2073	-0.0299	0.1836	-28.968	22.4139	-41.8182
19	3.8084	-0.2354	0.5175	3.7568	-0.7891	6.2616	-0.1516	0.3491	0.4258	-0.477	-0.1154	-0.3488	-0.5573	0.4017	0.1826	0.3906	-0.0477	0.0172	0.2506	0.0121	0.246	-27.5934	45.0378	-41.733
20	2.6197	-0.738	1.5649	2.3168	-2.6537	5.8225	-0.3834	0.4624	0.5312	-0.488	-0.6453	-0.3911	-0.9792	0.4709	0.9549	0.5359	-0.0792	-0.0504	0.46	0.0546	0.4408	-22.3893	45.8229	-33.8613
21	1.3806	0.233	0.1736	2.527	-0.2803	2.897	0.0025	-0.0739	0.1145	0.2201	-0.0603	-0.0067	-0.428	-0.0544	0.0616	0.1813	-0.0012	0.0004	0.2153	-0.0189	0.1436	-35.7298	36.9789	-36.5586
22	4.7029	0.4265	1.0673	1.1565	0.7627	2.2784	0.0587	-0.0431	-0.3436	-0.0746	0.0799	-0.443	0.0869	0.5122	-0.0768	0.2453	0.0038	0.0194	0.3363	0.0223	0.2788	-19.9887	27.6205	-43.1918
23	2.7624	0.4827	1.933	0.8247	0.5482	3.5798	0.1604	0.0448	-0.1871	-0.0557	-0.0359	-0.1511	0.1147	0.0701	-0.0912	0.1974	-0.0067	0.0152	0.1845	0.0173	0.1587	-29.2065	32.6403	-42.7968
24	1.8396	0.0955	0.7431	1.3177	-0.0454	2.7626	-0.1137	0.1734	0.0631	-0.1645	-0.0338	-0.1148	-0.3569	0.3644	0.1506	0.2623	-0.046	0.0224	0.2632	0.0191	0.1812	-24.2181	37.6644	-47.3177
25	4.8012	0.2862	0.6357	4.4453	-0.8981	3.6298	-0.157	-0.2604	0.0676	0.6948	0.1199	0.5941	-0.6484	-0.7266	0.0824	0.433	0.1102	0.0218	0.3093	0.0144	0.2784	-44.0429	43.1178	-45.7064
26	2.6175	-0.6096	-0.8071	2.4788	0.3277	4.2196	-0.1223	0.1374	-0.2432	-0.2136	-0.0668	0.3567	0.6284	-0.3005	0.1501	0.3405	-0.042	-0.0372	0.2366	-0.0073	0.2509	-42.3094	-9.7745	-57.2427
27	3.648	-2.2492	0.5467	2.3043	0.2673	2.8016	0.0346	0.3998	0.182	-0.2545	-0.1933	-0.0745	0.0618	-0.1446	0.1712	0.3521	0.0007	0.0079	0.2635	0.0283	0.2897	-38.3099	-2.6594	-53.0662
28	2.4738	-1.2253	-0.1347	3.9613	0.5981	2.8235	-0.0384	-0.1422	-0.0861	0.3687	-0.031	0.2556	0.4305	-0.0982	0.0518	0.3243	-0.0371	0.0109	0.2208	0.0181	0.212	-39.4016	-6.6733	-44.6781

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 4 through 35 )	A	4 - 35
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 36 through 78 )	A	36 - 78
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 79 through 125 )	A	79 - 125
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 126 through 165 )	A	126 - 165
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 4 through 23 )	B	4 - 23
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 24 through 42 )	B	24 - 42
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 43 through 67 )	B	43 - 67
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 68 through 99 )	B	68 - 99
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 100 through 149 )	B	100 - 149
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 150 through 164 )	B	150 - 164
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 4 through 29 )	C	4 - 29
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 30 through 119 )	C	30 - 119
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 120 through 160 )	C	120 - 160
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 4 through 35 )	D	4 - 35
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 36 through 83 )	D	36 - 83
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 84 through 120 )	D	84 - 120
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 121 through 125 )	D	121 - 125
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 126 through 165 )	D	126 - 165
19	X-RAY DIFFRACTION	19	chain 'E' and (resid 4 through 22 )	E	4 - 22
20	X-RAY DIFFRACTION	20	chain 'E' and (resid 23 through 42 )	E	23 - 42
21	X-RAY DIFFRACTION	21	chain 'E' and (resid 43 through 74 )	E	43 - 74
22	X-RAY DIFFRACTION	22	chain 'E' and (resid 75 through 93 )	E	75 - 93
23	X-RAY DIFFRACTION	23	chain 'E' and (resid 94 through 119 )	E	94 - 119
24	X-RAY DIFFRACTION	24	chain 'E' and (resid 120 through 149 )	E	120 - 149
25	X-RAY DIFFRACTION	25	chain 'E' and (resid 150 through 164 )	E	150 - 164
26	X-RAY DIFFRACTION	26	chain 'F' and (resid 7 through 29 )	F	7 - 29
27	X-RAY DIFFRACTION	27	chain 'F' and (resid 30 through 81 )	F	30 - 81
28	X-RAY DIFFRACTION	28	chain 'F' and (resid 82 through 159 )	F	82 - 159

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-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi