PDB-9gf2: CC-Hex-hen2 variant peptide with Hendecad repeat substitution

ID or keywords:

Entry

Database: PDB / ID: 9gf2

Title

CC-Hex-hen2 variant peptide with Hendecad repeat substitution

Components

CC-Hex2-hen2

Keywords

DE NOVO PROTEIN / Hendecad Repeat / Coiled-Coils / De novo Design

Biological species

synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / AB INITIO PHASING / Resolution: 2.099 Å

Authors

Kurgan, K.W. / Martin, F.J.O. / Woolfson, D.N.

Funding support

United States,

United Kingdom, 7items

Organization	Grant number	Country
National Science Foundation (NSF, United States)	BB/V004220/1	United States
Biotechnology and Biological Sciences Research Council (BBSRC)	BB/V004220/1	United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)	BB/R00661X/1	United Kingdom
Engineering and Physical Sciences Research Council	EP/G036764	United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)	BB/L01386X/1	United Kingdom
Royal Society	WM140008	United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)	BB/S002820/1	United Kingdom

Citation

Journal: Chem Sci / Year: 2025
Title: Exchange, promiscuity, and orthogonality in de novo designed coiled-coil peptide assemblies.
Authors: Kurgan, K.W. / Martin, F.J.O. / Dawson, W.M. / Brunnock, T. / Orr-Ewing, A.J. / Woolfson, D.N.

History

Deposition	Aug 8, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jan 22, 2025	Provider: repository / Type: Initial release
Revision 1.1	Jan 29, 2025	Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.2	Feb 5, 2025	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9gf2.cif.gz	82.5 KB	Display	PDBx/mmCIF format
PDB format	pdb9gf2.ent.gz	63.4 KB	Display	PDB format
PDBx/mmJSON format	9gf2.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/gf/9gf2 ftp://data.pdbj.org/pub/pdb/validation_reports/gf/9gf2	HTTPS FTP

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Related structure data

Related structure data	9gf3C 9gf4C 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 (2)

Deposited unit

A: CC-Hex2-hen2

B: CC-Hex2-hen2

C: CC-Hex2-hen2

D: CC-Hex2-hen2

E: CC-Hex2-hen2

F: CC-Hex2-hen2

hetero molecules

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

1

Idetical with deposited unit
defined by author
Evidence: equilibrium centrifugation

Unit cell

Length a, b, c (Å)	48.563, 58.157, 59.258
Angle α, β, γ (deg.)	90, 90, 90
Int Tables number	18
Space group name H-M	P22₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Beg auth comp-ID: LYS / Beg label comp-ID: LYS / Auth asym-ID: A / Label asym-ID: A

Dom-ID	Component-ID	Ens-ID	End auth comp-ID	End label comp-ID	Auth seq-ID	Label seq-ID
1	1	1	LYS	LYS	5 - 33	6 - 34
2	1	1	LYS	LYS	5 - 33	6 - 34
3	2	2	LYS	LYS	5 - 33	6 - 34
4	2	2	LYS	LYS	5 - 33	6 - 34
5	3	3	LYS	LYS	5 - 33	6 - 34
6	3	3	LYS	LYS	5 - 33	6 - 34
7	4	4	LEU	LEU	5 - 32	6 - 33
8	4	4	LEU	LEU	5 - 32	6 - 33
9	5	5	LYS	LYS	5 - 33	6 - 34
10	5	5	LYS	LYS	5 - 33	6 - 34

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6
4	Local NCS retraints between domains: 7 8
5	Local NCS retraints between domains: 9 10
6	Local NCS retraints between domains: 11 12
7	Local NCS retraints between domains: 13 14
8	Local NCS retraints between domains: 15 16
9	Local NCS retraints between domains: 17 18
10	Local NCS retraints between domains: 19 20
11	Local NCS retraints between domains: 21 22
12	Local NCS retraints between domains: 23 24
13	Local NCS retraints between domains: 25 26
14	Local NCS retraints between domains: 27 28
15	Local NCS retraints between domains: 29 30

#1: Protein/peptide	CC-Hex2-hen2 Mass: 3585.284 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical	ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₀H₂₂O₆ / Comment: precipitant*YM
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
Has protein modification	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 1.95 Å³/Da / Density % sol: 36.76 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2 M Ammonium Acetate, 0.1 M BIS-Tris, pH 5.5, 25% w/v PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
Detector	Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Oct 1, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 2.099→48.61 Å / Num. obs: 10287 / % possible obs: 100 % / Redundancy: 1.8 % / CC_1/2: 1 / R_merge(I) obs: 0.011 / R_pim(I) all: 0.011 / R_rim(I) all: 0.015 / Net I/σ(I): 26.6
Reflection shell	Resolution: 2.1→2.16 Å / Redundancy: 1.9 % / R_merge(I) obs: 0.071 / Mean I/σ(I) obs: 4.7 / Num. unique obs: 812 / CC_1/2: 0.986 / R_pim(I) all: 0.071 / R_rim(I) all: 0.101 / % possible all: 99.9

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0425	refinement
DIALS		data reduction
DIALS		data scaling
PHASER		phasing

Refinement

Method to determine structure: AB INITIO PHASING / Resolution: 2.099→48.61 Å / Cor.coef. F_o:F_c: 0.947 / Cor.coef. F_o:F_c free: 0.915 / SU B: 5.537 / SU ML: 0.154 / Cross valid method: FREE R-VALUE / ESU R: 0.284 / ESU R Free: 0.239
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2925	536	5.21 %
R_work	0.2236	9751	-
all	0.227	-	-
obs	-	10287	99.99 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 53.037 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.056 Å²	0 Å²	-0 Å²
2-	-	-0.433 Å²	0 Å²
3-	-	-	0.377 Å²

Refinement step

Cycle: LAST / Resolution: 2.099→48.61 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1372	0	16	38	1426

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.019	0.012	1393
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.016	1522
X-RAY DIFFRACTION	r_angle_refined_deg	2.694	1.83	1846
X-RAY DIFFRACTION	r_angle_other_deg	0.911	1.791	3543
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.216	5	184
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	19.335	10	299
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	13.397	10	25
X-RAY DIFFRACTION	r_chiral_restr	0.136	0.2	227
X-RAY DIFFRACTION	r_gen_planes_refined	0.012	0.02	1460
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	220
X-RAY DIFFRACTION	r_nbd_refined	0.242	0.2	378
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.196	0.2	1236
X-RAY DIFFRACTION	r_nbtor_refined	0.201	0.2	671
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.089	0.2	905
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.221	0.2	41
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.219	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.227	0.2	38
X-RAY DIFFRACTION	r_nbd_other	0.323	0.2	89
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.437	0.2	2
X-RAY DIFFRACTION	r_mcbond_it	9.165	4.853	754
X-RAY DIFFRACTION	r_mcbond_other	9.172	4.85	753
X-RAY DIFFRACTION	r_mcangle_it	11.806	8.602	932
X-RAY DIFFRACTION	r_mcangle_other	11.8	8.605	933
X-RAY DIFFRACTION	r_scbond_it	10.345	5.596	639
X-RAY DIFFRACTION	r_scbond_other	10.338	5.595	640
X-RAY DIFFRACTION	r_scangle_it	14.498	9.862	914
X-RAY DIFFRACTION	r_scangle_other	14.49	9.86	915
X-RAY DIFFRACTION	r_lrange_it	16.738	53.779	1647
X-RAY DIFFRACTION	r_lrange_other	16.743	53.829	1643
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.153	0.05	762
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.155	0.05	767
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.157	0.05	739
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.147	0.05	738
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.145	0.05	742
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.163	0.05	814
X-RAY DIFFRACTION	r_ncsr_local_group_7	0.178	0.05	756
X-RAY DIFFRACTION	r_ncsr_local_group_8	0.148	0.05	786
X-RAY DIFFRACTION	r_ncsr_local_group_9	0.172	0.05	849
X-RAY DIFFRACTION	r_ncsr_local_group_10	0.174	0.05	782
X-RAY DIFFRACTION	r_ncsr_local_group_11	0.142	0.05	782
X-RAY DIFFRACTION	r_ncsr_local_group_12	0.128	0.05	788
X-RAY DIFFRACTION	r_ncsr_local_group_13	0.163	0.05	733
X-RAY DIFFRACTION	r_ncsr_local_group_14	0.158	0.05	737
X-RAY DIFFRACTION	r_ncsr_local_group_15	0.14	0.05	761

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.15261	0.05006
1	2	A	X-RAY DIFFRACTION	Local ncs	0.15261	0.05006
2	3	A	X-RAY DIFFRACTION	Local ncs	0.15485	0.05006
2	4	A	X-RAY DIFFRACTION	Local ncs	0.15485	0.05006
3	5	A	X-RAY DIFFRACTION	Local ncs	0.15742	0.05006
3	6	A	X-RAY DIFFRACTION	Local ncs	0.15742	0.05006
4	7	A	X-RAY DIFFRACTION	Local ncs	0.14662	0.05006
4	8	A	X-RAY DIFFRACTION	Local ncs	0.14662	0.05006
5	9	A	X-RAY DIFFRACTION	Local ncs	0.14485	0.05006
5	10	A	X-RAY DIFFRACTION	Local ncs	0.14485	0.05006
6	11	A	X-RAY DIFFRACTION	Local ncs	0.16286	0.05006
6	12	A	X-RAY DIFFRACTION	Local ncs	0.16286	0.05006
7	13	A	X-RAY DIFFRACTION	Local ncs	0.17752	0.05006
7	14	A	X-RAY DIFFRACTION	Local ncs	0.17752	0.05006
8	15	A	X-RAY DIFFRACTION	Local ncs	0.14842	0.05006
8	16	A	X-RAY DIFFRACTION	Local ncs	0.14842	0.05006
9	17	A	X-RAY DIFFRACTION	Local ncs	0.17226	0.05005
9	18	A	X-RAY DIFFRACTION	Local ncs	0.17226	0.05005
10	19	A	X-RAY DIFFRACTION	Local ncs	0.17433	0.05007
10	20	A	X-RAY DIFFRACTION	Local ncs	0.17433	0.05007
11	21	A	X-RAY DIFFRACTION	Local ncs	0.14202	0.05007
11	22	A	X-RAY DIFFRACTION	Local ncs	0.14202	0.05007
12	23	A	X-RAY DIFFRACTION	Local ncs	0.12797	0.05006
12	24	A	X-RAY DIFFRACTION	Local ncs	0.12797	0.05006
13	25	A	X-RAY DIFFRACTION	Local ncs	0.1627	0.05006
13	26	A	X-RAY DIFFRACTION	Local ncs	0.1627	0.05006
14	27	A	X-RAY DIFFRACTION	Local ncs	0.15759	0.05006
14	28	A	X-RAY DIFFRACTION	Local ncs	0.15759	0.05006
15	29	A	X-RAY DIFFRACTION	Local ncs	0.13976	0.05006
15	30	A	X-RAY DIFFRACTION	Local ncs	0.13976	0.05006

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
2.099-2.153	0.289	32	0.193	698	0.197	731	0.959	0.977	99.8632	0.164
2.153-2.212	0.242	36	0.191	699	0.193	735	0.965	0.976	100	0.163
2.212-2.276	0.276	40	0.182	660	0.188	700	0.963	0.98	100	0.15
2.276-2.346	0.212	31	0.197	653	0.198	684	0.977	0.977	100	0.16
2.346-2.422	0.27	48	0.202	629	0.207	677	0.951	0.973	100	0.175
2.422-2.507	0.321	40	0.21	596	0.217	636	0.936	0.972	100	0.181
2.507-2.602	0.313	30	0.203	598	0.208	628	0.946	0.974	100	0.174
2.602-2.707	0.253	18	0.187	592	0.19	610	0.958	0.977	100	0.165
2.707-2.827	0.368	38	0.197	533	0.206	571	0.925	0.975	100	0.174
2.827-2.965	0.322	27	0.228	527	0.232	554	0.953	0.965	100	0.204
2.965-3.125	0.212	22	0.213	508	0.213	530	0.976	0.973	100	0.202
3.125-3.313	0.469	26	0.249	477	0.258	503	0.874	0.968	100	0.234
3.313-3.541	0.385	28	0.259	443	0.266	471	0.907	0.959	100	0.243
3.541-3.823	0.248	21	0.238	431	0.239	452	0.962	0.971	100	0.238
3.823-4.185	0.241	24	0.218	388	0.219	412	0.966	0.968	100	0.222
4.185-4.675	0.365	17	0.199	356	0.206	373	0.922	0.975	100	0.219
4.675-5.39	0.275	24	0.239	324	0.241	348	0.933	0.973	100	0.252
5.39-6.581	0.497	11	0.32	274	0.325	285	0.827	0.944	100	0.331
6.581-9.223	0.207	14	0.189	222	0.19	236	0.985	0.984	100	0.24
9.223-48.61	0.274	9	0.315	143	0.312	152	0.951	0.951	100	0.495

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