PDB-8qah: X-ray crystal structure of a de novo designed single-chain parall...

ID or keywords:

Entry

Database: PDB / ID: 8qah

Title

X-ray crystal structure of a de novo designed single-chain parallel coiled-coil alpha-helical barrel with 8 inner helices, sc-CC-8-58

Components

sc-CC-8-58

Keywords

DE NOVO PROTEIN / coiled coil / alpha-helical barrel / de novo protein design

Biological species

synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.35 Å

Authors

Petrenas, R. / Albanese, K.I. / Woolfson, D.N.

Funding support

United Kingdom, 1items

Citation

Journal: Nat.Chem.Biol. / Year: 2024
Title: Rationally seeded computational protein design of ɑ-helical barrels.
Authors: Albanese, K.I. / Petrenas, R. / Pirro, F. / Naudin, E.A. / Borucu, U. / Dawson, W.M. / Scott, D.A. / Leggett, G.J. / Weiner, O.D. / Oliver, T.A.A. / Woolfson, D.N.

History

Deposition	Aug 22, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 3, 2024	Provider: repository / Type: Initial release
Revision 1.1	Aug 7, 2024	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8qah.cif.gz	279.3 KB	Display	PDBx/mmCIF format
PDB format	pdb8qah.ent.gz	225.3 KB	Display	PDB format
PDBx/mmJSON format	8qah.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8qah_validation.pdf.gz	424.7 KB	Display	wwPDB validaton report
Full document	8qah_full_validation.pdf.gz	427.6 KB	Display
Data in XML	8qah_validation.xml.gz	26.5 KB	Display
Data in CIF	8qah_validation.cif.gz	38.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qa/8qah ftp://data.pdbj.org/pub/pdb/validation_reports/qa/8qah	HTTPS FTP

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Related structure data

Related structure data	8qaaC 8qabC 8qacC 8qadC 8qaeC 8qafC 8qagC 8qaiC 8qkdC 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: sc-CC-8-58

B: sc-CC-8-58

88.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: sc-CC-8-58

defined by author
Evidence: gel filtration, SAXS, equilibrium centrifugation
44.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: sc-CC-8-58

defined by author
Evidence: gel filtration, SAXS, equilibrium centrifugation
44.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	46.054, 78.587, 98.174
Angle α, β, γ (deg.)	90.00, 90.15, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	sc-CC-8-58 Mass: 44196.406 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 142 / 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: 2.01 Å³/Da / Density % sol: 38.8 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: Pact Premier D11: 0.2 M calcium chloride, 0.1 M TRIS, pH 8, 20 % w/v PEG 6000

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9999 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 25, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9999 Å / Relative weight: 1
Reflection	Resolution: 2.35→49.09 Å / Num. obs: 29247 / % possible obs: 99.56 % / Redundancy: 2 % / B_iso Wilson estimate: 14.18 Å² / CC_1/2: 0.988 / CC star: 0.997 / R_merge(I) obs: 0.09588 / R_pim(I) all: 0.09588 / R_rim(I) all: 0.1356 / Net I/σ(I): 5.98
Reflection shell	Resolution: 2.35→2.434 Å / Redundancy: 2 % / R_merge(I) obs: 0.4639 / Mean I/σ(I) obs: 1.81 / Num. unique obs: 2871 / CC_1/2: 0.681 / CC star: 0.9 / R_pim(I) all: 0.4639 / R_rim(I) all: 0.6561 / % possible all: 97.85

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Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
PHASER		phasing
AutoProcess		data reduction
AutoProcess		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.35→49.09 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.25 / Stereochemistry target values: ML
Details: Rotamer outliers and waters were fixed with COOT(0.8.9.2).

	R_factor	Num. reflection	% reflection
R_free	0.2323	1393	4.77 %
R_work	0.1906	-	-
obs	0.1926	29191	99.56 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 24.25 Å²

Refinement step

Cycle: LAST / Resolution: 2.35→49.09 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5392	0	0	142	5534

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	5415
X-RAY DIFFRACTION	f_angle_d	0.415	7432
X-RAY DIFFRACTION	f_dihedral_angle_d	3.33	884
X-RAY DIFFRACTION	f_chiral_restr	0.032	1037
X-RAY DIFFRACTION	f_plane_restr	0.003	931

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.35-2.43	0.3121	121	0.2466	2748	X-RAY DIFFRACTION	98
2.43-2.53	0.2409	158	0.2109	2757	X-RAY DIFFRACTION	100
2.53-2.65	0.2352	140	0.1883	2751	X-RAY DIFFRACTION	100
2.65-2.79	0.2309	158	0.1821	2768	X-RAY DIFFRACTION	100
2.79-2.96	0.2252	141	0.1844	2732	X-RAY DIFFRACTION	100
2.96-3.19	0.229	141	0.18	2801	X-RAY DIFFRACTION	100
3.19-3.51	0.2408	134	0.1911	2795	X-RAY DIFFRACTION	100
3.51-4.02	0.2312	130	0.1688	2783	X-RAY DIFFRACTION	100
4.02-5.06	0.2185	146	0.1755	2814	X-RAY DIFFRACTION	100
5.06-49.09	0.2112	124	0.2103	2849	X-RAY DIFFRACTION	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	3.5975	0.2622	-0.8534	1.2399	-0.0686	3.5767	0.0872	0.4771	0.3035	-0.2004	-0.0857	0.0104	-0.2328	-0.046	-0.0118	0.2703	-0.02	-0.0055	0.1355	0.0163	0.0609	4.6315	11.5568	25.2996
2	1.6237	-0.2394	-0.1514	0.3633	-0.1565	1.9531	0.0284	0.4385	0.0225	-0.2013	-0.0678	-0.0148	-0.03	0.0722	0.0091	0.3387	-0.0431	0.002	0.1933	-0.008	0.067	4.5326	4.652	20.0356
3	3.1324	0.7714	0.8884	0.7318	0.5196	2.6554	0.0959	0.401	-0.3559	-0.3322	0.005	-0.0391	0.2103	0.0715	-0.0716	0.2881	-0.0412	0.0093	0.1079	-0.033	0.1099	4.7911	-5.4094	24.3689
4	7.1006	0.0528	3.3107	2.5759	-0.2846	3.4803	0.026	0.2651	-0.6608	-0.2521	0.098	-0.0246	0.5291	0.0728	-0.1632	0.4207	-0.0293	0.0145	0.1114	-0.0157	0.2498	3.2679	-12.6101	31.8042
5	0.6919	0.0603	-0.1337	1.7492	-0.9099	1.7044	0.0462	-0.2075	-0.2539	-0.024	-0.0275	-0.1096	0.1783	-0.1124	0.0382	0.2128	-0.0487	-0.0311	0.1046	0.0563	0.1179	3.6253	-6.0819	42.1794
6	1.5176	-0.213	-0.1852	0.9262	-0.5564	2.245	-0.0514	-0.2481	-0.0679	0.172	-0.0094	-0.0166	-0.0165	-0.1239	-0.057	0.2059	-0.0536	-0.0293	0.162	0.0321	0.0496	3.8442	4.6509	49.2752
7	2.5226	-0.7107	0.0656	0.7594	0.3659	1.6051	-0.0011	-0.2841	0.1898	0.1963	-0.0285	-0.0626	-0.1494	0.0671	-0.0071	0.18	-0.0482	-0.0342	0.0776	0.012	0.0593	5.3701	14.8682	44.9713
8	4.2144	-0.3025	-1.5594	2.1117	0.0098	2.9788	0.0844	0.0696	0.3508	-0.0123	-0.1582	-0.0971	-0.1812	-0.041	0.0771	0.2035	-0.0299	-0.0448	0.0741	0.029	0.0884	4.2769	19.1112	35.715
9	2.4194	0.4173	0.374	1.5344	0.6994	1.9046	0.051	0.2343	-0.4546	-0.0758	0.0187	-0.1474	0.4185	0.0492	-0.0386	0.3363	-0.0108	0.039	0.1121	-0.0272	0.1277	-1.737	27.7813	8.8815
10	1.1838	-0.0794	0.5438	0.999	0.1443	2.7491	0.0878	0.4341	-0.099	-0.2416	-0.0413	-0.0073	0.2862	0.0056	-0.0619	0.3064	-0.0362	0.018	0.2398	0.0198	0.0653	-1.0702	36.7164	0.0981
11	0.7127	0.1248	0.1906	0.7523	-0.6275	1.8304	0.0066	0.2294	0.1875	-0.1309	0.0093	0.0044	-0.2076	-0.0879	-0.1794	0.3193	-0.0264	-0.0121	0.2225	0.0887	0.109	-1.6087	47.8716	2.1737
12	0.8275	-0.1432	0.3504	2.1432	-0.5485	1.2958	0.0622	0.2001	0.3877	-0.0817	-0.0009	-0.004	-0.3778	-0.027	-0.0098	0.2997	-0.0051	-0.0236	0.1274	0.1066	0.2187	-0.5834	53.7983	10.9275
13	1.7261	-0.4137	0.9635	2.252	0.374	0.7084	-0.036	-0.2164	0.5256	0.1776	0.0195	0.1787	-0.2331	0.0271	0.0376	0.2818	-0.014	0.0359	0.0769	-0.0258	0.1868	-1.6481	51.6442	22.1543
14	3.611	0.4275	0.7353	0.8498	0.2761	0.8742	-0.0106	-0.4822	0.2254	0.3168	-0.0752	0.0689	-0.1202	-0.0905	-0.0094	0.3033	0.0009	0.0174	0.0975	-0.0122	0.0887	-2.8178	42.6369	28.3984
15	5.6618	1.0789	1.4037	1.3865	-0.4224	2.1556	-0.0457	-0.3746	-0.2926	0.2526	0.0264	-0.0697	-0.088	-0.157	0.0895	0.3832	-0.0336	0.0376	0.1398	0.0397	0.1337	-2.1287	32.8179	30.6999
16	6.5971	1.9446	-0.0554	2.3856	-0.3433	1.6886	-0.0116	-0.2734	-0.3152	0.1571	-0.0419	-0.1358	0.2465	-0.0961	0.0289	0.2659	-0.0273	0.0297	0.0658	0.0008	0.0658	-2.5532	32.1917	22.8211

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid -1 through 27 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 28 through 84 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 85 through 139 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 140 through 168 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 169 through 255 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 256 through 312 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 313 through 367 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 368 through 424 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid -1 through 84 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 85 through 141 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 142 through 196 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 197 through 255 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 256 through 312 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 313 through 367 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 368 through 396 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 397 through 424 )

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