PDB-6g6c: Crystal structure of a parallel six-helix coiled coil CC-Type2-LL-L17E

ID or keywords:

Entry

Database: PDB / ID: 6g6c

Title

Crystal structure of a parallel six-helix coiled coil CC-Type2-LL-L17E

Components

CC-Type2-LL-L17E

Keywords

DE NOVO PROTEIN / de novo / coiled coil / alpha-helical bundle / synthetic construct

Biological species

synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.55 Å

Authors

Rhys, G.G. / Brady, R.L. / Woolfson, D.N.

Funding support

United Kingdom, 2items

Citation

Journal: Nat Commun / Year: 2018
Title: Maintaining and breaking symmetry in homomeric coiled-coil assemblies.
Authors: Rhys, G.G. / Wood, C.W. / Lang, E.J.M. / Mulholland, A.J. / Brady, R.L. / Thomson, A.R. / Woolfson, D.N.

History

Deposition	Apr 1, 2018	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Oct 17, 2018	Provider: repository / Type: Initial release
Revision 1.1	Nov 13, 2024	Group: Advisory / Data collection ...Advisory / Data collection / Database references / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6g6c.cif.gz	290.4 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	6g6c_validation.pdf.gz	584.6 KB	Display	wwPDB validaton report
Full document	6g6c_full_validation.pdf.gz	591.8 KB	Display
Data in XML	6g6c_validation.xml.gz	32.4 KB	Display
Data in CIF	6g6c_validation.cif.gz	46.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/g6/6g6c ftp://data.pdbj.org/pub/pdb/validation_reports/g6/6g6c	HTTPS FTP

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Related structure data

Related structure data	6g65C 6g66C 6g67C 6g68C 6g69C 6g6aC 6g6bC 6g6dC 6g6eC 6g6fC 6g6gC 6g6hC C: citing same article (ref.)
Similar structure data	7nxz-d 2dvp-d 5civ-d 4jue-3 6ebu-d 1a3s-d 4kbr-8 3a4s-1 3uv0-d 4a1k-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details)

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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: CC-Type2-LL-L17E

B: CC-Type2-LL-L17E

C: CC-Type2-LL-L17E

D: CC-Type2-LL-L17E

E: CC-Type2-LL-L17E

F: CC-Type2-LL-L17E

G: CC-Type2-LL-L17E

H: CC-Type2-LL-L17E

I: CC-Type2-LL-L17E

J: CC-Type2-LL-L17E

K: CC-Type2-LL-L17E

L: CC-Type2-LL-L17E

M: CC-Type2-LL-L17E

N: CC-Type2-LL-L17E

O: CC-Type2-LL-L17E

P: CC-Type2-LL-L17E

Q: CC-Type2-LL-L17E

R: CC-Type2-LL-L17E

S: CC-Type2-LL-L17E

T: CC-Type2-LL-L17E

U: CC-Type2-LL-L17E

V: CC-Type2-LL-L17E

W: CC-Type2-LL-L17E

X: CC-Type2-LL-L17E

78 kDa, 24 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: CC-Type2-LL-L17E

B: CC-Type2-LL-L17E

C: CC-Type2-LL-L17E

D: CC-Type2-LL-L17E

E: CC-Type2-LL-L17E

F: CC-Type2-LL-L17E

defined by software
Evidence: equilibrium centrifugation
19.5 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

G: CC-Type2-LL-L17E

H: CC-Type2-LL-L17E

I: CC-Type2-LL-L17E

J: CC-Type2-LL-L17E

K: CC-Type2-LL-L17E

L: CC-Type2-LL-L17E

defined by software
Evidence: equilibrium centrifugation
19.5 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

M: CC-Type2-LL-L17E

N: CC-Type2-LL-L17E

O: CC-Type2-LL-L17E

P: CC-Type2-LL-L17E

Q: CC-Type2-LL-L17E

R: CC-Type2-LL-L17E

defined by software
Evidence: equilibrium centrifugation
19.5 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

S: CC-Type2-LL-L17E

T: CC-Type2-LL-L17E

U: CC-Type2-LL-L17E

V: CC-Type2-LL-L17E

W: CC-Type2-LL-L17E

X: CC-Type2-LL-L17E

defined by software
Evidence: equilibrium centrifugation
19.5 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	45.319, 117.940, 59.240
Angle α, β, γ (deg.)	90.000, 101.240, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein/peptide	... CC-Type2-LL-L17E Mass: 3250.827 Da / Num. of mol.: 24 / Source method: obtained synthetically Details: solid-phase peptide synthesis using the fmoc-based strategy Source: (synth.) synthetic construct (others)
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 306 / Source method: isolated from a natural source / Formula: H₂O
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: 1.99 Å³/Da / Density % sol: 38.2 % / Mosaicity: 0.72 °
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 50 mM SPG Buffer (Succinic acid, Sodium phosphate monobasic monohydrate and Glycine) and 12.5% w/v PEG 1500

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Data collection

Diffraction

Mean temperature: 80 K

Diffraction source

Source:

SYNCHROTRON / Site:

Diamond

/ Beamline: I04 / Wavelength: 0.9795 Å

Detector

Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 18, 2016

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9795 Å / Relative weight: 1

Reflection

Resolution: 1.55→58.97 Å / Num. obs: 88233 / % possible obs: 100 % / Redundancy: 6 % / B_iso Wilson estimate: 18.99 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.071 / R_pim(I) all: 0.031 / R_rim(I) all: 0.077 / Net I/σ(I): 11.9 / Num. measured all: 525877 / Scaling rejects: 109

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	% possible all
1.55-1.58	6.1	0.831	4359	0.825	0.362	0.909	100
8.49-58.97	6.4	0.034	562	0.999	0.014	0.037	99.7

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

Model details: Phaser MODE: MR_AUTO

	Highest resolution	Lowest resolution
Rotation	7.14 Å	58.97 Å
Translation	7.14 Å	58.97 Å

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Processing

Software

Name	Version	Classification
iMOSFLM		data reduction
Aimless	0.5.28	data scaling
PHASER	2.6.1	phasing
PHENIX	1.9_1692	refinement
PDB_EXTRACT	3.24	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.55→58.97 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.57

	R_factor	Num. reflection	% reflection
R_free	0.2287	4473	5.07 %
R_work	0.1862	-	-
obs	0.1883	88141	99.92 %

Solvent computation

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

Displacement parameters

B_iso max: 121.55 Å² / B_iso mean: 28.6488 Å² / B_iso min: 12.76 Å²

Refinement step

Cycle: final / Resolution: 1.55→58.97 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5458	0	0	306	5764
B_iso mean	-	-	-	37.75	-
Num. residues	-	-	-	-	734

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.016	5791
X-RAY DIFFRACTION	f_angle_d	1.575	7779
X-RAY DIFFRACTION	f_chiral_restr	0.078	880
X-RAY DIFFRACTION	f_plane_restr	0.007	957
X-RAY DIFFRACTION	f_dihedral_angle_d	16.824	2282

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 (%)
1.55-1.5676	0.3247	141	0.2719	2832	2973	100
1.5676-1.586	0.3022	155	0.2574	2703	2858	100
1.586-1.6054	0.2945	178	0.247	2781	2959	100
1.6054-1.6257	0.2726	139	0.2391	2787	2926	100
1.6257-1.6471	0.2898	155	0.2375	2783	2938	100
1.6471-1.6697	0.2975	172	0.2425	2762	2934	100
1.6697-1.6935	0.2844	145	0.2382	2799	2944	100
1.6935-1.7188	0.2794	144	0.2324	2741	2885	100
1.7188-1.7457	0.2649	172	0.2184	2813	2985	100
1.7457-1.7743	0.2314	161	0.2037	2734	2895	100
1.7743-1.8049	0.2555	150	0.1999	2790	2940	100
1.8049-1.8377	0.2301	161	0.1958	2761	2922	100
1.8377-1.8731	0.2435	145	0.1986	2787	2932	100
1.8731-1.9113	0.2636	131	0.1951	2826	2957	100
1.9113-1.9529	0.2817	154	0.1922	2739	2893	100
1.9529-1.9983	0.2614	139	0.2021	2801	2940	100
1.9983-2.0483	0.2416	147	0.1979	2808	2955	100
2.0483-2.1036	0.2195	154	0.1893	2793	2947	100
2.1036-2.1655	0.1997	130	0.1858	2808	2938	100
2.1655-2.2354	0.2339	162	0.1819	2752	2914	100
2.2354-2.3153	0.2027	137	0.1754	2826	2963	100
2.3153-2.408	0.2219	130	0.1768	2808	2938	100
2.408-2.5176	0.2321	130	0.1686	2821	2951	100
2.5176-2.6504	0.2156	154	0.1801	2775	2929	100
2.6504-2.8164	0.213	154	0.1885	2808	2962	100
2.8164-3.0339	0.2305	157	0.181	2775	2932	100
3.0339-3.3392	0.2313	147	0.1827	2790	2937	100
3.3392-3.8223	0.1927	142	0.1703	2818	2960	100
3.8223-4.8153	0.2063	148	0.1565	2803	2951	100
4.8153-59.0127	0.2199	139	0.1862	2844	2983	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	2.2437	-0.7318	-0.4119	1.707	-0.1081	0.7493	-0.0023	-0.2411	-0.5232	0.0408	0.0305	0.0436	0.0628	0.0091	-0.035	0.1894	0.0166	0.0058	0.1475	0.0462	0.1461	32.7195	-8.0341	18.7696
2	4.7147	2.5977	-3.3695	2.8491	-1.7262	3.3671	0.1831	-0.4547	-0.4867	0.2967	-0.117	-0.1545	-0.2051	-0.0782	-0.0417	0.1867	0.033	-0.0173	0.2166	-0.0146	0.1306	33.2075	-1.461	23.5991
3	8.7825	1.1386	-1.3106	1.8415	0.0511	2.3617	-0.0515	-0.6656	0.3153	0.0058	0.0155	0.1713	-0.1935	0.0337	0.0164	0.2446	0.0287	-0.0096	0.1932	-0.0199	0.1481	30.6718	6.3224	23.298
4	5.5888	-0.5582	-1.7776	1.8128	0.0743	2.1215	0.0353	-0.3234	-0.147	0.0779	-0.0431	0.0544	0.2357	0.1016	0.0053	0.2499	-0.0112	0.0016	0.2088	-0.0495	0.1591	0.7802	-36.3864	22.7122
5	2.4231	-2.6012	-2.3635	3.6277	1.6108	3.38	0.3431	0.3522	-0.2104	-0.2971	-0.2077	0.1128	-0.1095	0.0533	-0.1477	0.1845	-0.0066	-0.006	0.1974	-0.0323	0.1151	1.7628	-30.5246	17.4223
6	8.979	-1.9419	-2.7601	2.1912	0.5671	3.1168	0.2794	0.3997	0.1001	-0.1917	-0.0776	-0.1121	-0.3417	0.1385	-0.1856	0.211	-0.0132	0.004	0.1825	-0.0015	0.1149	4.1467	-22.4676	17.7427
7	3.0206	0.6243	-1.9188	1.3696	0.3665	2.4841	0.0542	-0.0162	0.6499	-0.1134	0.143	-0.0436	-0.0681	0.0407	-0.1752	0.1768	-0.0052	-0.01	0.0845	0.0209	0.1358	31.2408	3.5798	11.9207
8	7.4234	-1.4455	-2.0158	0.6387	0.2291	1.5096	0.1238	0.2528	0.1383	-0.1101	-0.0343	0.0659	-0.0255	-0.1075	-0.1101	0.1962	-0.0235	-0.0235	0.142	0.001	0.1694	28.6026	-2.6912	7.5907
9	2.6399	-1.2626	0.0646	0.9838	0.0944	1.6235	-0.0168	0.0717	-0.56	0.0098	-0.0018	0.1872	0.2008	-0.1241	0.0286	0.2044	-0.0317	-0.0225	0.1341	0.0009	0.1864	27.2769	-10.5081	8.8871
10	1.8014	1.3229	-1.3547	2.0156	0.5326	3.3158	0.2968	-0.3343	0.6847	-0.1014	0.0128	0.1017	-0.5632	0.4965	-0.3179	0.2933	-0.0864	0.0084	0.2865	-0.0204	0.1535	2.975	-24.3003	29.3106
11	6.8141	0.6313	-0.5831	1.0678	0.1025	2.1182	0.2009	-0.3693	0.2951	0.1343	0.0406	-0.0229	-0.1758	0.6879	-0.147	0.1983	-0.0253	-0.01	0.3821	-0.0169	0.1319	5.2875	-30.6402	33.9622
12	3.1855	0.1205	-0.5151	1.3573	-0.332	1.8037	0.0642	-0.2406	-0.3745	0.0908	-0.139	-0.2523	0.4118	0.7824	0.0057	0.25	0.0814	-0.0083	0.4379	0.0677	0.2186	6.0387	-38.5521	33.0432
13	2.3264	-0.8022	-1.0193	1.6532	0.0008	2.8769	0.2288	-0.2964	0.0001	0.1527	-0.1017	0.0238	0.1611	0.2337	-0.1292	0.2357	0.016	-0.0234	0.1457	-0.0251	0.1199	2.7291	-36.0747	4.0491
14	2.4801	-0.9009	-2.6569	2.9315	0.472	3.4699	0.3688	-0.8038	0.4223	0.1571	-0.1184	-0.0205	-0.2371	0.3676	-0.2129	0.1652	-0.0126	-0.0041	0.1639	-0.0593	0.1602	2.533	-28.2037	2.1363
15	3.9247	-0.9302	0.0463	3.7269	-0.199	1.4111	0.0427	0.1434	0.6083	0.0216	0.0268	-0.0072	-0.1975	-0.1119	-0.0966	0.2161	-0.0034	0.004	0.1052	0.0158	0.2469	0.2239	-23.941	-4.6891
16	2.6547	-0.2725	-1.3894	2.134	0.6044	1.6043	0.1323	0.5076	0.4393	-0.1343	-0.0731	-0.0654	-0.0012	-0.0541	-0.0838	0.1842	0.0115	-0.0196	0.1622	0.0212	0.128	0.5907	-34.1559	-9.8251
17	2.8249	-2.5938	-1.0319	2.4878	0.5842	1.3489	0.1165	0.5934	-0.047	-0.1395	-0.1181	0.022	0.0736	-0.0676	0.0108	0.1723	-0.0321	0.0109	0.1483	-0.0149	0.2031	-1.5344	-41.3495	-7.484
18	2.3117	-0.5349	1.358	1.1528	0.0945	2.2763	0.0548	-0.4624	-0.4708	0.0868	0.0433	0.1303	0.2543	-0.1522	-0.1298	0.2124	-0.0131	0.0058	0.1328	-0.0036	0.2384	-3.1608	-45.2121	-0.7152
19	1.8427	0.2794	-1.2543	1.6247	-0.3979	3.4405	0.1855	0.6244	0.0535	-0.1866	0.0041	0.0573	0.1968	-0.4113	-0.1866	0.2078	-0.0063	-0.029	0.234	0.0481	0.1136	-2.6245	-5.203	-20.2888
20	1.7745	0.4672	-1.3603	1.9996	-0.091	2.9715	0.2961	0.4531	0.6534	-0.0738	-0.0083	0.0242	-0.2548	-0.1831	-0.2728	0.2127	0.023	-0.0107	0.2472	0.1203	0.2418	-1.8666	2.4937	-17.4369
21	2.1948	1.8482	-0.2636	3.8405	-1.6806	3.5376	0.3224	-0.0715	0.9233	0.2062	0.0549	0.1387	-0.3835	-0.1037	-0.361	0.2795	0.034	0.041	0.1216	0.0054	0.2692	0.1231	5.0039	-10.061
22	7.8939	1.304	-1.5471	1.8358	-0.3461	2.5939	0.1054	-0.2644	0.366	0.0713	-0.0224	0.0182	-0.1582	0.0228	-0.0949	0.2022	0.0217	-0.0172	0.1438	0.0009	0.1322	0.4547	-5.3233	-6.6421
23	6.1661	2.1066	-0.8559	2.6718	-0.5791	1.7275	0.0665	-0.0484	-0.402	0.0713	-0.078	-0.1885	0.0565	-0.0299	-0.0312	0.1715	0.0218	-0.0109	0.1088	-0.002	0.155	2.1133	-12.5122	-10.1185
24	2.4137	1.3052	1.2789	2.1719	0.4165	3.8111	0.0322	0.2541	-0.8499	-0.2134	0.0042	-0.1951	0.1724	-0.0429	-0.1185	0.1741	-0.0033	0.0106	0.1423	-0.0209	0.1925	4.5423	-14.7208	-17.1187

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'F' and (resid 1 through 30 )	F	1 - 30
2	X-RAY DIFFRACTION	2	chain 'E' and (resid 1 through 30 )	E	1 - 30
3	X-RAY DIFFRACTION	3	chain 'D' and (resid 1 through 30 )	D	1 - 30
4	X-RAY DIFFRACTION	4	chain 'U' and (resid 1 through 30 )	U	1 - 30
5	X-RAY DIFFRACTION	5	chain 'T' and (resid 1 through 29 )	T	1 - 29
6	X-RAY DIFFRACTION	6	chain 'S' and (resid 1 through 30 )	S	1 - 30
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 1 through 30 )	C	1 - 30
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 1 through 30 )	B	1 - 30
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 1 through 30 )	A	1 - 30
10	X-RAY DIFFRACTION	10	chain 'X' and (resid 1 through 30 )	X	1 - 30
11	X-RAY DIFFRACTION	11	chain 'W' and (resid 1 through 30 )	W	1 - 30
12	X-RAY DIFFRACTION	12	chain 'V' and (resid 1 through 30 )	V	1 - 30
13	X-RAY DIFFRACTION	13	chain 'R' and (resid 1 through 30 )	R	1 - 30
14	X-RAY DIFFRACTION	14	chain 'Q' and (resid 1 through 30 )	Q	1 - 30
15	X-RAY DIFFRACTION	15	chain 'P' and (resid 1 through 30 )	P	1 - 30
16	X-RAY DIFFRACTION	16	chain 'O' and (resid 1 through 30 )	O	1 - 30
17	X-RAY DIFFRACTION	17	chain 'N' and (resid 1 through 30 )	N	1 - 30
18	X-RAY DIFFRACTION	18	chain 'M' and (resid 1 through 30 )	M	1 - 30
19	X-RAY DIFFRACTION	19	chain 'I' and (resid 1 through 30 )	I	1 - 30
20	X-RAY DIFFRACTION	20	chain 'H' and (resid 1 through 30 )	H	1 - 30
21	X-RAY DIFFRACTION	21	chain 'G' and (resid 2 through 30 )	G	2 - 30
22	X-RAY DIFFRACTION	22	chain 'L' and (resid 1 through 29 )	L	1 - 29
23	X-RAY DIFFRACTION	23	chain 'K' and (resid 1 through 29 )	K	1 - 29
24	X-RAY DIFFRACTION	24	chain 'J' and (resid 1 through 29 )	J	1 - 29

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