PDB-6g69: Crystal structure of a parallel seven-helix coiled coil CC-Type2-...

ID or keywords:

Entry

Database: PDB / ID: 6g69

Title

Crystal structure of a parallel seven-helix coiled coil CC-Type2-IL-Sg-L17E

Components

CC-Type2-IL-Sg-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: 2.2 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	Jan 23, 2019	Group: Data collection / Derived calculations / Category: pdbx_data_processing_status / struct_conn

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6g69.cif.gz	183.4 KB	Display	PDBx/mmCIF format
PDB format	pdb6g69.ent.gz	158.6 KB	Display	PDB format
PDBx/mmJSON format	6g69.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6g69_validation.pdf.gz	548.1 KB	Display	wwPDB validaton report
Full document	6g69_full_validation.pdf.gz	568.9 KB	Display
Data in XML	6g69_validation.xml.gz	18.9 KB	Display
Data in CIF	6g69_validation.cif.gz	26.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/g6/6g69 ftp://data.pdbj.org/pub/pdb/validation_reports/g6/6g69	HTTPS FTP

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Related structure data

Related structure data	6g65C 6g66C 6g67C 6g68C 6g6aC 6g6bC 6g6cC 6g6dC 6g6eC 6g6fC 6g6gC 6g6hC C: citing same article (ref.)
Similar structure data	5eza-d 6g66-d 4pna-d 5ezc-d 6cay-3 7baw-d 5ez9-d 1vj2-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)

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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-IL-Sg-L17E

B: CC-Type2-IL-Sg-L17E

C: CC-Type2-IL-Sg-L17E

D: CC-Type2-IL-Sg-L17E

E: CC-Type2-IL-Sg-L17E

F: CC-Type2-IL-Sg-L17E

G: CC-Type2-IL-Sg-L17E

H: CC-Type2-IL-Sg-L17E

I: CC-Type2-IL-Sg-L17E

J: CC-Type2-IL-Sg-L17E

K: CC-Type2-IL-Sg-L17E

L: CC-Type2-IL-Sg-L17E

M: CC-Type2-IL-Sg-L17E

N: CC-Type2-IL-Sg-L17E

hetero molecules

47 kDa, 14 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: CC-Type2-IL-Sg-L17E

B: CC-Type2-IL-Sg-L17E

C: CC-Type2-IL-Sg-L17E

D: CC-Type2-IL-Sg-L17E

E: CC-Type2-IL-Sg-L17E

F: CC-Type2-IL-Sg-L17E

G: CC-Type2-IL-Sg-L17E

hetero molecules

defined by software
Evidence: equilibrium centrifugation
23.4 kDa, 7 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

H: CC-Type2-IL-Sg-L17E

I: CC-Type2-IL-Sg-L17E

J: CC-Type2-IL-Sg-L17E

K: CC-Type2-IL-Sg-L17E

L: CC-Type2-IL-Sg-L17E

M: CC-Type2-IL-Sg-L17E

N: CC-Type2-IL-Sg-L17E

hetero molecules

defined by software
Evidence: equilibrium centrifugation
23.6 kDa, 7 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	66.770, 66.770, 243.197
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	146
Space group name H-M	H3

Components on special symmetry positions

ID	Model	Components
1	1	I-103- HOH

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:
NCS ensembles :

#1: Protein/peptide	CC-Type2-IL-Sg-L17E Mass: 3314.827 Da / Num. of mol.: 14 / Source method: obtained synthetically Details: solid-phase peptide synthesis using the fmoc-based strategy Source: (synth.) synthetic construct (others)
#2: Chemical	ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₆H₁₄O₂ / Comment: precipitant*YM
#3: Chemical	ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₄O₂ / Comment: precipitant*YM
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 15 / 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: 2.25 Å³/Da / Density % sol: 45.29 % / Mosaicity: 0.38 °
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 100 mM Ammonium Phosphate monobasic, 50 mM Tris and 25% v/v MPD

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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: 2.2→56.26 Å / Num. obs: 20520 / % possible obs: 99.9 % / Redundancy: 9.3 % / CC_1/2: 0.999 / R_merge(I) obs: 0.061 / R_pim(I) all: 0.021 / R_rim(I) all: 0.065 / Net I/σ(I): 16.4

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
2.2-2.27	9.4	1.134	1786	0.552	0.385	1.198	99.6
9.07-56.26	9.6	0.032	302	0.999	0.01	0.033	99.8

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

Model details: Phaser MODE: MR_AUTO

	Highest resolution	Lowest resolution
Rotation	3.32 Å	56.26 Å
Translation	3.32 Å	56.26 Å

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Processing

Software

Name	Version	Classification
iMOSFLM		data reduction
Aimless	0.5.27	data scaling
PHASER	2.6.1	phasing
REFMAC	5.8.0189	refinement
PDB_EXTRACT	3.24	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.2→56.26 Å / Cor.coef. F_o:F_c: 0.954 / Cor.coef. F_o:F_c free: 0.932 / SU B: 19.326 / SU ML: 0.213 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.375 / ESU R Free: 0.263
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2762	1105	5.4 %	RANDOM
R_work	0.2069	-	-	-
obs	0.2106	19415	99.8 %	-

Solvent computation

Ion probe radii: 1.2 Å / Shrinkage radii: 1.2 Å / VDW probe radii: 1.3 Å

Displacement parameters

B_iso max: 169.5 Å² / B_iso mean: 71.681 Å² / B_iso min: 26.06 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.57 Å²	0.29 Å²	0 Å²
2-	-	0.57 Å²	0 Å²
3-	-	-	-1.85 Å²

Refinement step

Cycle: final / Resolution: 2.2→56.26 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3196	0	40	15	3251
B_iso mean	-	-	95.84	78.05	-
Num. residues	-	-	-	-	419

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.023	0.02	3516
X-RAY DIFFRACTION	r_bond_other_d	0.003	0.02	3644
X-RAY DIFFRACTION	r_angle_refined_deg	2.442	2.004	4673
X-RAY DIFFRACTION	r_angle_other_deg	1.084	2.999	8555
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.472	5	443
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	39.621	27.756	127
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	19.497	15	806
X-RAY DIFFRACTION	r_chiral_restr	0.117	0.2	538
X-RAY DIFFRACTION	r_gen_planes_refined	0.011	0.02	3636
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	532

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	B	1804	0.11
1	2	C	1804	0.11
2	1	B	1762	0.14
2	2	D	1762	0.14
3	1	B	1808	0.11
3	2	E	1808	0.11
4	1	B	1790	0.12
4	2	F	1790	0.12
5	1	B	1756	0.16
5	2	G	1756	0.16
6	1	B	1708	0.15
6	2	H	1708	0.15
7	1	B	1790	0.13
7	2	I	1790	0.13
8	1	B	1770	0.13
8	2	J	1770	0.13
9	1	B	1808	0.09
9	2	K	1808	0.09
10	1	B	1790	0.12
10	2	L	1790	0.12
11	1	B	1758	0.15
11	2	M	1758	0.15
12	1	B	1428	0.15
12	2	N	1428	0.15
13	1	C	1784	0.11
13	2	D	1784	0.11
14	1	C	1800	0.11
14	2	E	1800	0.11
15	1	C	1782	0.1
15	2	F	1782	0.1
16	1	C	1760	0.16
16	2	G	1760	0.16
17	1	C	1684	0.15
17	2	H	1684	0.15
18	1	C	1780	0.13
18	2	I	1780	0.13
19	1	C	1758	0.14
19	2	J	1758	0.14
20	1	C	1742	0.12
20	2	K	1742	0.12
21	1	C	1810	0.11
21	2	L	1810	0.11
22	1	C	1762	0.14
22	2	M	1762	0.14
23	1	C	1428	0.14
23	2	N	1428	0.14
24	1	D	1762	0.11
24	2	E	1762	0.11
25	1	D	1756	0.1
25	2	F	1756	0.1
26	1	D	1730	0.15
26	2	G	1730	0.15
27	1	D	1658	0.13
27	2	H	1658	0.13
28	1	D	1746	0.13
28	2	I	1746	0.13
29	1	D	1764	0.12
29	2	J	1764	0.12
30	1	D	1718	0.11
30	2	K	1718	0.11
31	1	D	1796	0.1
31	2	L	1796	0.1
32	1	D	1780	0.14
32	2	M	1780	0.14
33	1	D	1424	0.11
33	2	N	1424	0.11
34	1	E	1764	0.09
34	2	F	1764	0.09
35	1	E	1746	0.15
35	2	G	1746	0.15
36	1	E	1678	0.11
36	2	H	1678	0.11
37	1	E	1790	0.08
37	2	I	1790	0.08
38	1	E	1740	0.11
38	2	J	1740	0.11
39	1	E	1744	0.11
39	2	K	1744	0.11
40	1	E	1788	0.09
40	2	L	1788	0.09
41	1	E	1746	0.12
41	2	M	1746	0.12
42	1	E	1396	0.12
42	2	N	1396	0.12
43	1	F	1756	0.14
43	2	G	1756	0.14
44	1	F	1690	0.13
44	2	H	1690	0.13
45	1	F	1756	0.11
45	2	I	1756	0.11
46	1	F	1742	0.12
46	2	J	1742	0.12
47	1	F	1736	0.11
47	2	K	1736	0.11
48	1	F	1800	0.1
48	2	L	1800	0.1
49	1	F	1780	0.12
49	2	M	1780	0.12
50	1	F	1434	0.12
50	2	N	1434	0.12
51	1	G	1710	0.13
51	2	H	1710	0.13
52	1	G	1768	0.15
52	2	I	1768	0.15
53	1	G	1760	0.15
53	2	J	1760	0.15
54	1	G	1752	0.14
54	2	K	1752	0.14
55	1	G	1806	0.14
55	2	L	1806	0.14
56	1	G	1818	0.12
56	2	M	1818	0.12
57	1	G	1430	0.15
57	2	N	1430	0.15
58	1	H	1666	0.12
58	2	I	1666	0.12
59	1	H	1660	0.13
59	2	J	1660	0.13
60	1	H	1620	0.13
60	2	K	1620	0.13
61	1	H	1654	0.14
61	2	L	1654	0.14
62	1	H	1668	0.13
62	2	M	1668	0.13
63	1	H	1380	0.14
63	2	N	1380	0.14
64	1	I	1766	0.14
64	2	J	1766	0.14
65	1	I	1770	0.11
65	2	K	1770	0.11
66	1	I	1798	0.13
66	2	L	1798	0.13
67	1	I	1784	0.14
67	2	M	1784	0.14
68	1	I	1462	0.12
68	2	N	1462	0.12
69	1	J	1716	0.13
69	2	K	1716	0.13
70	1	J	1768	0.12
70	2	L	1768	0.12
71	1	J	1782	0.13
71	2	M	1782	0.13
72	1	J	1424	0.13
72	2	N	1424	0.13
73	1	K	1706	0.12
73	2	L	1706	0.12
74	1	K	1690	0.13
74	2	M	1690	0.13
75	1	K	1362	0.13
75	2	N	1362	0.13
76	1	L	1800	0.12
76	2	M	1800	0.12
77	1	L	1440	0.13
77	2	N	1440	0.13
78	1	M	1412	0.14
78	2	N	1412	0.14

LS refinement shell

Resolution: 2.2→2.257 Å / R_factor R_free error: 0 / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.365	83	-
R_work	0.294	1439	-
all	-	1522	-
obs	-	-	99.54 %

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	2.1311	-1.4633	2.4145	6.4962	-8.2536	11.7681	-0.0442	0.2467	-0.1586	-0.0848	-0.0253	-0.2827	0.0054	0.2289	0.0695	0.093	-0.0491	0.0615	0.1297	-0.0176	0.2388	55.418	63.024	1.103
2	2.3862	0.4697	-0.7725	2.3585	-4.5873	8.9933	-0.0785	0.0627	-0.2554	-0.0885	0.0564	-0.0575	0.0749	-0.0939	0.0221	0.1956	-0.0724	0.0661	0.1461	-0.0322	0.2047	47.969	59.845	1.635
3	8.5603	-4.6323	6.7973	6.74	-8.5191	11.2088	-0.5101	-0.3421	0.6373	0.2334	0.0164	-0.5679	-0.4784	-0.0248	0.4937	0.2076	-0.0567	-0.0166	0.0684	-0.026	0.3942	56.013	74.101	9.389
4	2.6165	-4.0652	3.292	9.3584	-9.1621	11.4081	-0.1593	0.1422	0.1335	-0.0788	-0.0067	-0.4037	0.0132	0.2911	0.166	0.0731	-0.0874	0.0211	0.1492	0.0332	0.2745	58.745	68.054	5.015
5	1.4615	-0.1179	0.3883	2.7383	-3.3498	11.182	-0.1019	0.1092	-0.0989	-0.0772	0.0547	0.165	0.3193	-0.3834	0.0473	0.0865	-0.0814	-0.001	0.1962	-0.0057	0.1717	41.345	63.866	3.355
6	2.7568	-0.9407	3.1666	2.0986	-2.8699	8.3558	-0.0488	0.0381	0.1964	0.0593	0.146	0.0582	0.0261	-0.1787	-0.0972	0.1015	-0.0284	-0.0042	0.2001	0.0242	0.1701	40.08	71.019	6.05
7	2.2678	-1.7479	0.4048	3.3864	-4.5222	9.1054	0.1558	-0.1641	0.4136	-0.1255	0.0812	-0.3028	-0.0713	-0.1759	-0.237	0.1498	0.0609	0.0642	0.1921	0.1236	0.3342	48.102	58.623	50.227
8	1.3505	-1.4142	0.4661	7.4496	-9.5383	15.1022	0.0894	-0.2707	0.4736	-0.0373	-0.1502	-0.753	-0.2212	0.1863	0.0607	0.0579	0.0275	0.0803	0.2007	0.0747	0.3826	55.697	58.436	49.671
9	4.7537	-0.7608	-6.394	4.4647	-2.5748	11.8417	0.2118	0.0859	-0.5316	-0.6051	-0.5603	0.1186	0.1561	0.0906	0.3484	0.1012	0.0682	0.0155	0.3335	0.2595	0.5037	42.599	46.326	46.649
10	2.1155	-0.1524	-2.0904	2.9035	-3.4622	7.452	0.1466	-0.1336	-0.0505	-0.2562	-0.1923	0.0435	-0.0173	-0.1344	0.0457	0.1375	0.0849	-0.0256	0.3366	-0.0051	0.1637	42.587	53.671	48.766
11	2.2575	1.0205	-2.5906	12.3342	-10.8215	11.4304	0.2058	-0.0204	0.3742	-0.2358	-0.0061	-1.0066	0.1357	-0.0164	-0.1998	0.1119	0.0989	-0.0243	0.1785	0.094	1.0498	60.788	52.992	47.241
12	7.1067	6.609	-5.3298	10.2947	-11.3707	13.9306	0.3314	0.3612	-0.5224	0.1647	0.0193	-0.0536	-0.0813	0.1846	-0.3507	0.2134	0.147	0.21	0.1177	0.0902	0.4168	59.058	46.874	42.985
13	9.7958	5.2399	-10.353	3.3293	-7.6072	21.0015	0.5159	-0.1451	-0.8379	-0.0266	-0.2572	-0.2543	-0.0839	0.3765	-0.2587	0.4888	0.2647	0.0226	0.1984	0.0062	0.3097	51.976	43.78	40.891
14	4.9109	-1.352	4.3934	3.5077	-5.9012	10.9591	-0.6457	-0.2866	0.6234	0.4688	0.2653	-0.0569	-0.9847	-0.5251	0.3804	0.2135	0.0758	-0.0681	0.1005	-0.0533	0.2802	47.474	76.056	10.728

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	E	1 - 30
2	X-RAY DIFFRACTION	2	D	1 - 30
3	X-RAY DIFFRACTION	3	G	1 - 30
4	X-RAY DIFFRACTION	4	F	1 - 30
5	X-RAY DIFFRACTION	5	C	1 - 30
6	X-RAY DIFFRACTION	6	B	1 - 30
7	X-RAY DIFFRACTION	7	K	1 - 30
8	X-RAY DIFFRACTION	8	J	1 - 29
9	X-RAY DIFFRACTION	9	M	1 - 30
10	X-RAY DIFFRACTION	10	L	1 - 30
11	X-RAY DIFFRACTION	11	I	1 - 30
12	X-RAY DIFFRACTION	12	H	2 - 29
13	X-RAY DIFFRACTION	13	N	5 - 30
14	X-RAY DIFFRACTION	14	A	1 - 30

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Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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+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

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Movie

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Structure viewers

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Viewer log

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This page

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This web site

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Options

+
Open data

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Basic information

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Structure visualization

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Downloads & links

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Download

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Validation report

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Related structure data

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Links

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Assembly

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Components

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Experimental details

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Experiment

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Sample preparation

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Data collection

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Phasing

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Processing

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About Yorodumi

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News

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

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Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

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

+
Jul 12, 2017. Major update of PDB

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Yorodumi