PDB-7qwe: CC-Type2-(Ug)4

Basic information

• Entry: Database: PDB / ID: 7qwe
• Title: CC-Type2-(Ug)4
• Components: CC-Type2-(Ug)4
• Keywords: DE NOVO PROTEIN / aib / coiled coil / pentamer / 2-Aminoisobutyric acid
• Biological species: synthetic construct (others)
• Method: X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.34 Å
• Authors: Martin, F.J.O. / Zieleniewski, F. / Dawson, W.M. / Woolfson, D.N.

Funding support

United Kingdom, 3items

Organization	Grant number	Country
European Research Council (ERC)	340764	United Kingdom
Engineering and Physical Sciences Research Council	EP/G036764	United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)	BB R00661X 1	United Kingdom

• Citation: Journal: To Be Published; Title: CC-Type2-(Ug)4; Authors: Martin, F.J.O. / Zieleniewski, F. / Dawson, W.M. / Woolfson, D.N.

History

Deposition	Jan 25, 2022	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Feb 1, 2023	Provider: repository / Type: Initial release

Assembly

Deposited unit

A: CC-Type2-(Ug)4

B: CC-Type2-(Ug)4

C: CC-Type2-(Ug)4

D: CC-Type2-(Ug)4

E: CC-Type2-(Ug)4

F: CC-Type2-(Ug)4

G: CC-Type2-(Ug)4

H: CC-Type2-(Ug)4

I: CC-Type2-(Ug)4

J: CC-Type2-(Ug)4

Summary:

• 33.3 kDa, 10 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	33,308	10
Polymers	33,308	10
Non-polymers	0	0
Water	2,126	118

1

A: CC-Type2-(Ug)4

B: CC-Type2-(Ug)4

D: CC-Type2-(Ug)4

F: CC-Type2-(Ug)4

J: CC-Type2-(Ug)4

Summary:

• defined by author
• Evidence: equilibrium centrifugation
• 16.7 kDa, 5 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	16,654	5
Polymers	16,654	5
Non-polymers	0	0
Water	90	5

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1
crystal symmetry operation	1_655	x+1,y,z	1

Calculated values:

Buried area	7120 Å2
ΔGint	-87 kcal/mol
Surface area	7870 Å2

2

E: CC-Type2-(Ug)4

H: CC-Type2-(Ug)4

G: CC-Type2-(Ug)4

I: CC-Type2-(Ug)4

C: CC-Type2-(Ug)4

Summary:

• defined by author
• 16.7 kDa, 5 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	16,654	5
Polymers	16,654	5
Non-polymers	0	0
Water	90	5

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1
crystal symmetry operation	1_655	x+1,y,z	1
crystal symmetry operation	1_455	x-1,y,z	1
crystal symmetry operation	3_646	-x+1,y-1/2,-z+3/2	1

Calculated values:

Buried area	6770 Å2
ΔGint	-84 kcal/mol
Surface area	7950 Å2

Unit cell

Length a, b, c (Å)	45.871, 58.490, 110.765
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P212121

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
1	2	A
2	2	C
1	3	A
2	3	D
1	4	A
2	4	E
1	5	A
2	5	F
1	6	A
2	6	G
1	7	A
2	7	H
1	8	A
2	8	I
1	9	A
2	9	J
1	10	B
2	10	C
1	11	B
2	11	D
1	12	B
2	12	E
1	13	B
2	13	F
1	14	B
2	14	G
1	15	B
2	15	H
1	16	B
2	16	I
1	17	B
2	17	J
1	18	C
2	18	D
1	19	C
2	19	E
1	20	C
2	20	F
1	21	C
2	21	G
1	22	C
2	22	H
1	23	C
2	23	I
1	24	C
2	24	J
1	25	D
2	25	E
1	26	D
2	26	F
1	27	D
2	27	G
1	28	D
2	28	H
1	29	D
2	29	I
1	30	D
2	30	J
1	31	E
2	31	F
1	32	E
2	32	G
1	33	E
2	33	H
1	34	E
2	34	I
1	35	E
2	35	J
1	36	F
2	36	G
1	37	F
2	37	H
1	38	F
2	38	I
1	39	F
2	39	J
1	40	G
2	40	H
1	41	G
2	41	I
1	42	G
2	42	J
1	43	H
2	43	I
1	44	H
2	44	J
1	45	I
2	45	J

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	0	1	0	A	1 - 30
2	0	1	0	B	1 - 30
1	0	2	0	A	1 - 30
2	0	2	0	C	1 - 30
1	0	3	0	A	1 - 30
2	0	3	0	D	1 - 30
1	0	4	0	A	1 - 30
2	0	4	0	E	1 - 30
1	0	5	0	A	1 - 30
2	0	5	0	F	1 - 30
1	0	6	0	A	1 - 28
2	0	6	0	G	1 - 28
1	0	7	0	A	2 - 29
2	0	7	0	H	2 - 29
1	0	8	0	A	1 - 30
2	0	8	0	I	1 - 30
1	0	9	0	A	2 - 29
2	0	9	0	J	2 - 29
1	0	10	0	B	1 - 30
2	0	10	0	C	1 - 30
1	0	11	0	B	1 - 30
2	0	11	0	D	1 - 30
1	0	12	0	B	1 - 30
2	0	12	0	E	1 - 30
1	0	13	0	B	1 - 30
2	0	13	0	F	1 - 30
1	0	14	0	B	1 - 28
2	0	14	0	G	1 - 28
1	0	15	0	B	2 - 29
2	0	15	0	H	2 - 29
1	0	16	0	B	1 - 30
2	0	16	0	I	1 - 30
1	0	17	0	B	2 - 29
2	0	17	0	J	2 - 29
1	0	18	0	C	1 - 30
2	0	18	0	D	1 - 30
1	0	19	0	C	1 - 30
2	0	19	0	E	1 - 30
1	0	20	0	C	1 - 30
2	0	20	0	F	1 - 30
1	0	21	0	C	1 - 28
2	0	21	0	G	1 - 28
1	0	22	0	C	2 - 29
2	0	22	0	H	2 - 29
1	0	23	0	C	1 - 30
2	0	23	0	I	1 - 30
1	0	24	0	C	2 - 29
2	0	24	0	J	2 - 29
1	0	25	0	D	1 - 30
2	0	25	0	E	1 - 30
1	0	26	0	D	1 - 30
2	0	26	0	F	1 - 30
1	0	27	0	D	1 - 28
2	0	27	0	G	1 - 28
1	0	28	0	D	2 - 29
2	0	28	0	H	2 - 29
1	0	29	0	D	1 - 30
2	0	29	0	I	1 - 30
1	0	30	0	D	2 - 29
2	0	30	0	J	2 - 29
1	0	31	0	E	1 - 30
2	0	31	0	F	1 - 30
1	0	32	0	E	1 - 28
2	0	32	0	G	1 - 28
1	0	33	0	E	2 - 29
2	0	33	0	H	2 - 29
1	0	34	0	E	1 - 30
2	0	34	0	I	1 - 30
1	0	35	0	E	2 - 29
2	0	35	0	J	2 - 29
1	0	36	0	F	1 - 28
2	0	36	0	G	1 - 28
1	0	37	0	F	2 - 29
2	0	37	0	H	2 - 29
1	0	38	0	F	1 - 30
2	0	38	0	I	1 - 30
1	0	39	0	F	2 - 29
2	0	39	0	J	2 - 29
1	0	40	0	G	2 - 28
2	0	40	0	H	2 - 28
1	0	41	0	G	1 - 28
2	0	41	0	I	1 - 28
1	0	42	0	G	2 - 28
2	0	42	0	J	2 - 28
1	0	43	0	H	2 - 29
2	0	43	0	I	2 - 29
1	0	44	0	H	2 - 30
2	0	44	0	J	2 - 30
1	0	45	0	I	2 - 29
2	0	45	0	J	2 - 29

NCS ensembles :

ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45

Components

#1: Protein/peptide

A B C D E F G H I J
CC-Type2-(Ug)4

Details:

Mass: 3330.839 Da / Num. of mol.: 10 / Mutation: W19BrPhe / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

#2: Water

ChemComp-HOH / water

Details:

Mass: 18.015 Da / Num. of mol.: 118 / Source method: isolated from a natural source / Formula: H₂O

• Has ligand of interest: N

Experimental details

Experiment

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

Sample preparation

• Crystal: Density Matthews: 2.23 ų/Da / Density % sol: 44.86 %
• Crystal grow: Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 ; Details: 1.5 mM peptide, 50 mM Sodium HEPES, 10 % w/v PEG 4000, and 5 % v/v 2-Propanol, at pH 7.5.

Data collection

• Diffraction: Mean temperature: 100 K / Serial crystal experiment: N
• Diffraction source: Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.919 Å
• Detector: Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 16, 2020
• Radiation: Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
• Radiation wavelength: Wavelength: 0.919 Å / Relative weight: 1
• Reflection: Resolution: 1.34→42.42 Å / Num. obs: 67638 / % possible obs: 99.79 % / Redundancy: 50.1 % / B_iso Wilson estimate: 13.7 Ų / CC_1/2: 1 / CC star: 1 / R_merge(I) obs: 0.2081 / R_pim(I) all: 0.02952 / R_rim(I) all: 0.2102 / Net I/σ(I): 8.23
• Reflection shell: Resolution: 1.341→1.389 Å / Redundancy: 49.9 % / Num. unique obs: 6657 / CC_1/2: 0.211 / CC star: 0.59 / R_pim(I) all: 2.984 / R_rim(I) all: 21.31 / % possible all: 99.48

Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
PDB_EXTRACT	3.27	data extraction
DIALS		data reduction
Aimless		data scaling
SHELXDE		phasing

Refinement

Method to determine structure: SAD / Resolution: 1.34→42.42 Å / Cor.coef. F_o:F_c: 0.966 / Cor.coef. F_o:F_c free: 0.961 / WR_factor R_free: 0.2269 / WR_factor R_work: 0.1943 / FOM work R set: 0.6504 / SU B: 4.656 / SU ML: 0.073 / SU R Cruickshank DPI: 0.0659 / SU R_free: 0.0621 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.066 / ESU R Free: 0.062 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED

	Rfactor	Num. reflection	% reflection	Selection details
Rfree	0.237	3457	5.1 %	RANDOM
Rwork	0.2054	-	-	-
obs	0.207	64179	99.96 %	-

• Solvent computation: Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK

Displacement parameters

B_iso max: 63 Ų / B_iso mean: 26.296 Ų / B_iso min: 14.26 Ų

	Baniso -1	Baniso -2	Baniso -3
1-	-3.31 Å2	0 Å2	0 Å2
2-	-	3.48 Å2	0 Å2
3-	-	-	-0.17 Å2

Refinement step

Cycle: final / Resolution: 1.34→42.42 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2251	0	0	118	2369
Biso mean	-	-	-	35.02	-
Num. residues	-	-	-	-	300

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.013	2251
X-RAY DIFFRACTION	r_bond_other_d	0.003	0.017	2545
X-RAY DIFFRACTION	r_angle_refined_deg	1.347	1.634	3060
X-RAY DIFFRACTION	r_angle_other_deg	1.236	1.586	5803
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	3.779	5	284
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	40.931	28.81	63
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.13	15	476
X-RAY DIFFRACTION	r_chiral_restr	0.072	0.2	280
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	2377
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	367
X-RAY DIFFRACTION	r_rigid_bond_restr	3.09	3	4796

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	A	823	0.13
1	2	B	823	0.13
2	1	A	818	0.14
2	2	C	818	0.14
3	1	A	815	0.13
3	2	D	815	0.13
4	1	A	807	0.13
4	2	E	807	0.13
5	1	A	804	0.14
5	2	F	804	0.14
6	1	A	784	0.13
6	2	G	784	0.13
7	1	A	790	0.15
7	2	H	790	0.15
8	1	A	828	0.11
8	2	I	828	0.11
9	1	A	783	0.15
9	2	J	783	0.15
10	1	B	853	0.11
10	2	C	853	0.11
11	1	B	830	0.1
11	2	D	830	0.1
12	1	B	803	0.14
12	2	E	803	0.14
13	1	B	805	0.14
13	2	F	805	0.14
14	1	B	794	0.11
14	2	G	794	0.11
15	1	B	800	0.13
15	2	H	800	0.13
16	1	B	837	0.11
16	2	I	837	0.11
17	1	B	780	0.13
17	2	J	780	0.13
18	1	C	818	0.13
18	2	D	818	0.13
19	1	C	809	0.13
19	2	E	809	0.13
20	1	C	809	0.13
20	2	F	809	0.13
21	1	C	781	0.13
21	2	G	781	0.13
22	1	C	796	0.14
22	2	H	796	0.14
23	1	C	832	0.13
23	2	I	832	0.13
24	1	C	783	0.13
24	2	J	783	0.13
25	1	D	800	0.13
25	2	E	800	0.13
26	1	D	806	0.13
26	2	F	806	0.13
27	1	D	813	0.06
27	2	G	813	0.06
28	1	D	799	0.12
28	2	H	799	0.12
29	1	D	829	0.09
29	2	I	829	0.09
30	1	D	788	0.12
30	2	J	788	0.12
31	1	E	814	0.1
31	2	F	814	0.1
32	1	E	765	0.13
32	2	G	765	0.13
33	1	E	771	0.15
33	2	H	771	0.15
34	1	E	805	0.13
34	2	I	805	0.13
35	1	E	767	0.15
35	2	J	767	0.15
36	1	F	770	0.13
36	2	G	770	0.13
37	1	F	777	0.14
37	2	H	777	0.14
38	1	F	817	0.13
38	2	I	817	0.13
39	1	F	771	0.15
39	2	J	771	0.15
40	1	G	772	0.13
40	2	H	772	0.13
41	1	G	796	0.1
41	2	I	796	0.1
42	1	G	761	0.13
42	2	J	761	0.13
43	1	H	799	0.13
43	2	I	799	0.13
44	1	H	816	0.09
44	2	J	816	0.09
45	1	I	783	0.14
45	2	J	783	0.14

LS refinement shell

Resolution: 1.341→1.375 Å / R_factor R_free error: 0 / Total num. of bins used: 20

	Rfactor	Num. reflection	% reflection
Rfree	0.398	243	-
Rwork	0.398	4688	-
all	-	4931	-
obs	-	-	99.5 %

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	10.5388	-2.0272	-2.6709	1.5908	1.1267	3.5118	-0.03	0.6174	0.0602	-0.1789	-0.0683	-0.0288	-0.0119	-0.2602	0.0983	0.216	-0.0182	0.0111	0.0508	-0.0173	0.0554	6.9597	4.0297	93.6459
2	14.6082	-2.7255	-5.1157	1.2728	1.0909	3.489	0.0724	0.5598	0.5719	-0.0446	-0.0005	-0.0266	-0.1876	-0.0647	-0.0719	0.1908	0.0007	-0.0047	0.0568	0.0215	0.0686	8.0465	9.7131	99.3129
3	12.6798	2.7868	0.7666	2.5185	0.3838	2.4375	0.0446	-0.426	-0.2493	0.0945	-0.0229	-0.1159	0.2248	0.1168	-0.0217	0.2173	0.0093	0.0242	0.0589	-0.0054	0.0734	26.1923	2.6776	80.1488
4	13.2089	-0.765	0.2008	1.7987	0.19	2.0769	0.0096	0.1633	-0.433	-0.0434	-0.0387	-0.0115	0.1988	0.0429	0.0291	0.2191	-0.0052	0.0324	0.005	-0.0134	0.0847	10.8114	-2.3389	102.0398
5	9.7278	-1.7705	-0.8663	3.3377	0.2003	2.8771	0.0138	0.2283	0.6459	0.1845	-0.0441	-0.0301	-0.2262	-0.1376	0.0303	0.2423	0.0171	-0.0115	0.0339	-0.016	0.145	24.8187	-15.2104	94.1766
6	11.2722	2.2528	-1.5711	1.2664	-0.3592	2.1854	0.0674	-0.5349	-0.0073	0.118	-0.1043	0.0791	0.1096	0.1342	0.0369	0.2148	0.0155	0.0095	0.0283	0.0031	0.0762	13.1553	1.3665	110.5288
7	12.6983	0.7733	1.588	2.0979	-0.2116	2.9778	0.033	-0.3517	0.0339	0.2507	-0.009	0.0299	0.0467	-0.0943	-0.024	0.2459	0.0269	0.033	0.0713	-0.0032	0.0589	-23.9077	-23.6078	97.9473
8	14.2603	-2.9045	-2.3377	2.6237	0.505	2.6011	0.061	0.2113	0.5087	-0.0819	0.0145	0.1008	-0.1581	-0.1398	-0.0755	0.2006	-0.0005	-0.0095	0.082	0.0248	0.1089	20.6096	-18.549	87.0215
9	12.7555	-1.5913	4.188	1.8018	-0.4186	2.8934	0.1005	0.1305	-0.7535	-0.0128	0.0315	0.2015	0.3156	-0.0647	-0.132	0.2522	-0.0276	0.0287	0.1142	0.039	0.1446	64.4751	-32.1638	91.7804
10	12.5244	0.8135	-1.2566	1.0578	-0.3255	2.0972	0.0763	-0.3005	0.206	0.1087	-0.0989	0.0359	-0.1424	0.026	0.0226	0.1814	-0.0004	-0.0033	0.0165	-0.019	0.0611	-36.7492	8.3844	107.3728

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 30
2	X-RAY DIFFRACTION	2	B	0 - 30
3	X-RAY DIFFRACTION	3	C	1 - 30
4	X-RAY DIFFRACTION	4	D	1 - 30
5	X-RAY DIFFRACTION	5	E	1 - 30
6	X-RAY DIFFRACTION	6	F	0 - 30
7	X-RAY DIFFRACTION	7	G	0 - 29
8	X-RAY DIFFRACTION	8	H	2 - 30
9	X-RAY DIFFRACTION	9	I	1 - 30
10	X-RAY DIFFRACTION	10	J	2 - 30