PDB-7bau: A de novo pentameric coiled-coil assembly: CC-Type2-(TgIaId)4-W19...

ID or keywords:

Entry

Database: PDB / ID: 7bau

Title

A de novo pentameric coiled-coil assembly: CC-Type2-(TgIaId)4-W19BrPhe.

Components

CC-Type2-(TgLaId)4-W19BrPhe.

Keywords

DE NOVO PROTEIN / alpha / helical / barrel / pentamer

Biological species

synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.42 Å

Authors

Martin, F.J.O. / Dawson, W.M. / Shelley, K. / Brady, R.L. / 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: Chem Sci / Year: 2021
Title: Coiled coils 9-to-5: rational de novo design of alpha-helical barrels with tunable oligomeric states.
Authors: Dawson, W.M. / Martin, F.J.O. / Rhys, G.G. / Shelley, K.L. / Brady, R.L. / Woolfson, D.N.

History

Deposition	Dec 16, 2020	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Apr 28, 2021	Provider: repository / Type: Initial release
Revision 1.1	Nov 17, 2021	Group: Data collection / Database references / Structure summary Category: citation / citation_author ...citation / citation_author / database_2 / diffrn_source / pdbx_database_proc / struct Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct.pdbx_center_of_mass_x / _struct.pdbx_center_of_mass_y / _struct.pdbx_center_of_mass_z
Revision 1.2	Jan 31, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _diffrn_source.pdbx_synchrotron_site / _struct_ncs_dom_lim.beg_auth_comp_id ..._diffrn_source.pdbx_synchrotron_site / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7bau.cif.gz	131.2 KB	Display	PDBx/mmCIF format
PDB format	pdb7bau.ent.gz	105.8 KB	Display	PDB format
PDBx/mmJSON format	7bau.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/ba/7bau ftp://data.pdbj.org/pub/pdb/validation_reports/ba/7bau	HTTPS FTP

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Related structure data

Related structure data	7a1tC 7basC 7batC 7bavC 7bawC 7bimC 4pndS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4pnd-d 4kvv-2 7bav-d 3r48-d 6q5n-2 7bas-d 4pn8-2 6q5n-1 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-(TgLaId)4-W19BrPhe.

B: CC-Type2-(TgLaId)4-W19BrPhe.

C: CC-Type2-(TgLaId)4-W19BrPhe.

D: CC-Type2-(TgLaId)4-W19BrPhe.

E: CC-Type2-(TgLaId)4-W19BrPhe.

F: CC-Type2-(TgLaId)4-W19BrPhe.

G: CC-Type2-(TgLaId)4-W19BrPhe.

H: CC-Type2-(TgLaId)4-W19BrPhe.

I: CC-Type2-(TgLaId)4-W19BrPhe.

J: CC-Type2-(TgLaId)4-W19BrPhe.

33.9 kDa, 10 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: CC-Type2-(TgLaId)4-W19BrPhe.

B: CC-Type2-(TgLaId)4-W19BrPhe.

C: CC-Type2-(TgLaId)4-W19BrPhe.

D: CC-Type2-(TgLaId)4-W19BrPhe.

E: CC-Type2-(TgLaId)4-W19BrPhe.

defined by author&software
Evidence: equilibrium centrifugation
17 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

F: CC-Type2-(TgLaId)4-W19BrPhe.

G: CC-Type2-(TgLaId)4-W19BrPhe.

H: CC-Type2-(TgLaId)4-W19BrPhe.

I: CC-Type2-(TgLaId)4-W19BrPhe.

J: CC-Type2-(TgLaId)4-W19BrPhe.

defined by author&software
17 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	40.597, 53.446, 56.156
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: _ / Refine code: _

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

NCS ensembles :

#1: Protein/peptide	CC-Type2-(TgLaId)4-W19BrPhe. Mass: 3394.835 Da / Num. of mol.: 10 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 184 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	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: 1.79 Å³/Da / Density % sol: 31.46 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 650 mM peptide, 1.0 M Ammonium formate 50 mM Sodium HEPES Temp details: 20 degC incubator

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

Diamond

/ Beamline: I24 / Wavelength: 0.92 Å

Detector

Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 7, 2020

Radiation

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

Radiation wavelength

Wavelength: 0.92 Å / Relative weight: 1

Reflection

Resolution: 1.42→40.63 Å / Num. obs: 42429 / % possible obs: 99.9 % / Redundancy: 6.7 % / CC_1/2: 0.996 / R_merge(I) obs: 0.13 / R_pim(I) all: 0.082 / R_rim(I) all: 0.154 / Net I/σ(I): 7.8

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
7.79-40.6	10.1	0.077	301	0.998	0.025	0.081
1.42-1.45	10.5	3.396	2171	0.496	1.083	3.568	96.3

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Processing

Software

Name	Version	Classification
Aimless	0.7.4	data scaling
REFMAC	5.8.0258	refinement
PDB_EXTRACT	3.25	data extraction
DIALS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4PND

4pnd

Resolution: 1.42→40.6 Å / Cor.coef. F_o:F_c: 0.964 / Cor.coef. F_o:F_c free: 0.947 / SU B: 3.512 / SU ML: 0.059 / SU R Cruickshank DPI: 0.0894 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.089 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2255	2341	5.2 %	RANDOM
R_work	0.1767	-	-	-
obs	0.179	42429	98.81 %	-

Solvent computation

Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.3 Å / Solvent model: MASK

Displacement parameters

B_iso max: 56.72 Å² / B_iso mean: 18.766 Å² / B_iso min: 9.98 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.85 Å²	-0 Å²	0.33 Å²
2-	-	-0.22 Å²	0 Å²
3-	-	-	-0.63 Å²

Refinement step

Cycle: final / Resolution: 1.42→40.6 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2271	0	0	184	2455
B_iso mean	-	-	-	28.78	-
Num. residues	-	-	-	-	305

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.013	2277
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.018	2465
X-RAY DIFFRACTION	r_angle_refined_deg	1.555	1.659	2983
X-RAY DIFFRACTION	r_angle_other_deg	11.278	1.597	5700
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.447	5	267
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.54	28.361	61
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.899	15	491
X-RAY DIFFRACTION	r_chiral_restr	0.093	0.2	402
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	2202
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	310
X-RAY DIFFRACTION	r_rigid_bond_restr	3.171	3	4742

Refine LS restraints NCS

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

LS refinement shell

Resolution: 1.422→1.459 Å / R_factor R_free error: 0 / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.304	191	-
R_work	0.275	3070	-
all	-	3261	-
obs	-	-	96.79 %

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	15.0762	-3.2119	3.0517	1.3532	-0.7992	1.2263	0.0176	0.0946	-0.1106	-0.1059	0.0144	0.0935	0.0932	-0.1206	-0.032	0.0269	-0.0138	-0.0178	0.0459	-0.0164	0.0415	40.4887	-6.5176	19.4591
2	13.5515	-3.108	-0.5469	2.7555	0.1585	2.0505	0.0301	0.1578	0.0903	-0.0688	0.0026	-0.085	0.0213	0.1142	-0.0326	0.003	0.0024	0.0004	0.0141	-0.0052	0.0056	39.6657	2.5295	16.8276
3	14.7451	-0.0832	-3.5725	0.5167	0.0988	1.6161	0.0429	0.1743	0.1905	0.0135	0.0038	-0.0361	-0.1309	0.0207	-0.0467	0.0233	-0.0059	-0.006	0.0131	-0.005	0.0142	39.8002	7.1935	24.6159
4	14.0323	2.4859	2.7964	1.149	0.3302	1.295	0.0398	-0.3871	-0.1792	0.0701	-0.0414	-0.0661	0.1128	-0.0121	0.0016	0.0262	0.0135	0.0015	0.02	0.0013	0.0354	40.1443	-7.3129	28.0819
5	15.4483	4.4021	-1.8084	1.4906	-0.4665	0.7762	0.0381	-0.0895	-0.0552	0.1072	0.001	0.0111	0.0094	-0.0364	-0.0391	0.0397	0.0113	0.0095	0.0085	0.0074	0.0199	40.2948	1.5701	31.702
6	14.6019	0.3258	3.5192	0.788	0.1162	1.5437	0.0294	0.227	-0.2564	-0.0052	0.0212	0.043	0.1355	-0.0123	-0.0505	0.0252	-0.0101	0.0024	0.0142	-0.0011	0.0097	20.9954	-5.0763	-3.5039
7	14.3586	-3.4437	0.5607	2.6782	-0.0996	2.0044	0.0073	0.1676	-0.1846	-0.0732	0.0192	0.121	-0.025	-0.1353	-0.0265	0.004	0.0018	-0.0013	0.0196	0.0053	0.008	20.6372	-0.2971	-11.3119
8	15.005	-2.9533	-3.2569	1.1812	0.6891	1.2511	0.0184	0.2164	0.1777	-0.0973	0.004	-0.0942	-0.0797	0.0796	-0.0224	0.0281	-0.0148	0.0095	0.0483	0.0139	0.0466	20.1185	8.7987	-8.8353
9	14.5337	2.4151	-3.0459	1.0458	-0.332	1.4456	0.035	-0.2949	0.1376	0.0396	-0.0379	0.0469	-0.1092	0.0015	0.0029	0.0185	0.0085	-0.006	0.0123	0.0008	0.0381	21.2002	9.5124	-0.307
10	15.1893	4.2869	1.571	1.4698	0.6429	0.8514	-0.0151	-0.0019	0.0747	0.0919	0.0409	-0.0132	-0.0019	0.0601	-0.0258	0.0459	0.0111	-0.013	0.0088	-0.0031	0.0169	20.7839	0.5503	3.4419

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	0 - 29
2	X-RAY DIFFRACTION	2	B	2 - 30
3	X-RAY DIFFRACTION	3	C	2 - 31
4	X-RAY DIFFRACTION	4	D	1 - 31
5	X-RAY DIFFRACTION	5	E	0 - 31
6	X-RAY DIFFRACTION	6	F	2 - 31
7	X-RAY DIFFRACTION	7	G	1 - 30
8	X-RAY DIFFRACTION	8	H	0 - 30
9	X-RAY DIFFRACTION	9	I	1 - 31
10	X-RAY DIFFRACTION	10	J	0 - 30

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