PDB-6q5n: Crystal structure of a CC-Hex mutant that forms a parallel six-he...

ID or keywords:

Entry

Database: PDB / ID: 6q5n

Title

Crystal structure of a CC-Hex mutant that forms a parallel six-helix coiled coil CC-Hex*-L24Nle

Components

CC-Hex*-L24Nle

Keywords

DE NOVO PROTEIN / coiled coil / hexamer / synthetic / cc-hex

Function / homology

1,4-DIETHYLENE DIOXIDE

Function and homology information

Biological species

synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

Wood, C.W. / Beesley, J.L. / Rhys, G.G. / Brady, R.L. / Woolfson, D.N.

Funding support

United Kingdom,

Belgium, 5items

Organization	Grant number	Country
Biotechnology and Biological Sciences Research Council	BB/J014400/1	United Kingdom
Engineering and Physical Sciences Research Council	EP/G036764/1	United Kingdom
European Research Council	340764	Belgium
Biotechnology and Biological Sciences Research Council	BB/R00661X/1	United Kingdom
Engineering and Physical Sciences Research Council	EP/K03927X/1	United Kingdom

Citation

Journal: J.Am.Chem.Soc. / Year: 2019
Title: Navigating the Structural Landscape of De Novo alpha-Helical Bundles.
Authors: Rhys, G.G. / Wood, C.W. / Beesley, J.L. / Zaccai, N.R. / Burton, A.J. / Brady, R.L. / Thomson, A.R. / Woolfson, D.N.

History

Deposition	Dec 9, 2018	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 22, 2019	Provider: repository / Type: Initial release
Revision 1.1	Jun 19, 2019	Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2	Nov 13, 2024	Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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	6q5n.cif.gz	87.6 KB	Display	PDBx/mmCIF format
PDB format	pdb6q5n.ent.gz	68.1 KB	Display	PDB format
PDBx/mmJSON format	6q5n.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6q5n_validation.pdf.gz	520.1 KB	Display	wwPDB validaton report
Full document	6q5n_full_validation.pdf.gz	525.1 KB	Display
Data in XML	6q5n_validation.xml.gz	16.1 KB	Display
Data in CIF	6q5n_validation.cif.gz	23 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/q5/6q5n ftp://data.pdbj.org/pub/pdb/validation_reports/q5/6q5n	HTTPS FTP

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Related structure data

Related structure data	6q5hC 6q5iC 6q5jC 6q5kC 6q5lC 6q5mC 6q5oC 6q5pC 6q5qC 6q5rC 6q5sC C: citing same article (ref.)
Similar structure data	3r47-1 4kvv-2 2rem-2 3r48-d 4kvu-1 4kvt-d 2w2r-d 2xgw-d 6q5j-d 3ron-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) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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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-Hex*-L24Nle

B: CC-Hex*-L24Nle

C: CC-Hex*-L24Nle

D: CC-Hex*-L24Nle

E: CC-Hex*-L24Nle

F: CC-Hex*-L24Nle

G: CC-Hex*-L24Nle

H: CC-Hex*-L24Nle

I: CC-Hex*-L24Nle

J: CC-Hex*-L24Nle

K: CC-Hex*-L24Nle

L: CC-Hex*-L24Nle

hetero molecules

39.9 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: CC-Hex*-L24Nle

B: CC-Hex*-L24Nle

C: CC-Hex*-L24Nle

D: CC-Hex*-L24Nle

E: CC-Hex*-L24Nle

F: CC-Hex*-L24Nle

hetero molecules

defined by author&software
Evidence: equilibrium centrifugation
20.1 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

G: CC-Hex*-L24Nle

H: CC-Hex*-L24Nle

I: CC-Hex*-L24Nle

J: CC-Hex*-L24Nle

K: CC-Hex*-L24Nle

L: CC-Hex*-L24Nle

hetero molecules

defined by author&software
Evidence: equilibrium centrifugation
19.9 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	54.190, 59.290, 143.770
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: _ / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / Refine code: _

Dom-ID	Ens-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	GLY	GLY	A	A	1 - 30	2 - 31
2	1	GLY	GLY	B	B	1 - 30	2 - 31
1	2	ALA	ALA	A	A	1 - 28	2 - 29
2	2	ALA	ALA	C	C	1 - 28	2 - 29
1	3	ALA	ALA	A	A	1 - 28	2 - 29
2	3	ALA	ALA	D	D	1 - 28	2 - 29
1	4	ALA	ALA	A	A	1 - 28	2 - 29
2	4	ALA	ALA	E	E	1 - 28	2 - 29
1	5	GLY	GLY	A	A	1 - 30	2 - 31
2	5	GLY	GLY	F	F	1 - 30	2 - 31
1	6	ALA	ALA	A	A	1 - 28	2 - 29
2	6	ALA	ALA	G	G	1 - 28	2 - 29
1	7	GLY	GLY	A	A	1 - 30	2 - 31
2	7	GLY	GLY	H	H	1 - 30	2 - 31
1	8	GLY	GLY	A	A	1 - 30	2 - 31
2	8	GLY	GLY	I	I	1 - 30	2 - 31
1	9	GLY	GLY	A	A	1 - 30	2 - 31
2	9	GLY	GLY	J	J	1 - 30	2 - 31
1	10	GLY	GLY	A	A	1 - 30	2 - 31
2	10	GLY	GLY	K	K	1 - 30	2 - 31
1	11	GLY	GLY	A	A	1 - 30	2 - 31
2	11	GLY	GLY	L	L	1 - 30	2 - 31
1	12	ALA	ALA	B	B	1 - 28	2 - 29
2	12	ALA	ALA	C	C	1 - 28	2 - 29
1	13	ALA	ALA	B	B	1 - 28	2 - 29
2	13	ALA	ALA	D	D	1 - 28	2 - 29
1	14	ALA	ALA	B	B	1 - 28	2 - 29
2	14	ALA	ALA	E	E	1 - 28	2 - 29
1	15	GLY	GLY	B	B	1 - 30	2 - 31
2	15	GLY	GLY	F	F	1 - 30	2 - 31
1	16	ALA	ALA	B	B	1 - 28	2 - 29
2	16	ALA	ALA	G	G	1 - 28	2 - 29
1	17	GLY	GLY	B	B	1 - 30	2 - 31
2	17	GLY	GLY	H	H	1 - 30	2 - 31
1	18	GLY	GLY	B	B	1 - 30	2 - 31
2	18	GLY	GLY	I	I	1 - 30	2 - 31
1	19	GLY	GLY	B	B	1 - 30	2 - 31
2	19	GLY	GLY	J	J	1 - 30	2 - 31
1	20	GLY	GLY	B	B	1 - 30	2 - 31
2	20	GLY	GLY	K	K	1 - 30	2 - 31
1	21	GLY	GLY	B	B	1 - 30	2 - 31
2	21	GLY	GLY	L	L	1 - 30	2 - 31
1	22	GLN	GLN	C	C	1 - 29	2 - 30
2	22	GLN	GLN	D	D	1 - 29	2 - 30
1	23	GLN	GLN	C	C	1 - 29	2 - 30
2	23	GLN	GLN	E	E	1 - 29	2 - 30
1	24	ALA	ALA	C	C	1 - 28	2 - 29
2	24	ALA	ALA	F	F	1 - 28	2 - 29
1	25	GLN	GLN	C	C	1 - 29	2 - 30
2	25	GLN	GLN	G	G	1 - 29	2 - 30
1	26	ALA	ALA	C	C	1 - 28	2 - 29
2	26	ALA	ALA	H	H	1 - 28	2 - 29
1	27	ALA	ALA	C	C	1 - 28	2 - 29
2	27	ALA	ALA	I	I	1 - 28	2 - 29
1	28	ALA	ALA	C	C	1 - 28	2 - 29
2	28	ALA	ALA	J	J	1 - 28	2 - 29
1	29	ALA	ALA	C	C	1 - 28	2 - 29
2	29	ALA	ALA	K	K	1 - 28	2 - 29
1	30	ALA	ALA	C	C	1 - 28	2 - 29
2	30	ALA	ALA	L	L	1 - 28	2 - 29
1	31	GLN	GLN	D	D	1 - 29	2 - 30
2	31	GLN	GLN	E	E	1 - 29	2 - 30
1	32	ALA	ALA	D	D	1 - 28	2 - 29
2	32	ALA	ALA	F	F	1 - 28	2 - 29
1	33	GLN	GLN	D	D	1 - 29	2 - 30
2	33	GLN	GLN	G	G	1 - 29	2 - 30
1	34	ALA	ALA	D	D	1 - 28	2 - 29
2	34	ALA	ALA	H	H	1 - 28	2 - 29
1	35	ALA	ALA	D	D	1 - 28	2 - 29
2	35	ALA	ALA	I	I	1 - 28	2 - 29
1	36	ALA	ALA	D	D	1 - 28	2 - 29
2	36	ALA	ALA	J	J	1 - 28	2 - 29
1	37	ALA	ALA	D	D	1 - 28	2 - 29
2	37	ALA	ALA	K	K	1 - 28	2 - 29
1	38	ALA	ALA	D	D	1 - 28	2 - 29
2	38	ALA	ALA	L	L	1 - 28	2 - 29
1	39	ALA	ALA	E	E	1 - 28	2 - 29
2	39	ALA	ALA	F	F	1 - 28	2 - 29
1	40	GLN	GLN	E	E	1 - 29	2 - 30
2	40	GLN	GLN	G	G	1 - 29	2 - 30
1	41	ALA	ALA	E	E	1 - 28	2 - 29
2	41	ALA	ALA	H	H	1 - 28	2 - 29
1	42	ALA	ALA	E	E	1 - 28	2 - 29
2	42	ALA	ALA	I	I	1 - 28	2 - 29
1	43	ALA	ALA	E	E	1 - 28	2 - 29
2	43	ALA	ALA	J	J	1 - 28	2 - 29
1	44	ALA	ALA	E	E	1 - 28	2 - 29
2	44	ALA	ALA	K	K	1 - 28	2 - 29
1	45	ALA	ALA	E	E	1 - 28	2 - 29
2	45	ALA	ALA	L	L	1 - 28	2 - 29
1	46	ALA	ALA	F	F	1 - 28	2 - 29
2	46	ALA	ALA	G	G	1 - 28	2 - 29
1	47	GLY	GLY	F	F	1 - 30	2 - 31
2	47	GLY	GLY	H	H	1 - 30	2 - 31
1	48	GLY	GLY	F	F	1 - 30	2 - 31
2	48	GLY	GLY	I	I	1 - 30	2 - 31
1	49	GLY	GLY	F	F	1 - 30	2 - 31
2	49	GLY	GLY	J	J	1 - 30	2 - 31
1	50	GLY	GLY	F	F	1 - 30	2 - 31
2	50	GLY	GLY	K	K	1 - 30	2 - 31
1	51	GLY	GLY	F	F	1 - 30	2 - 31
2	51	GLY	GLY	L	L	1 - 30	2 - 31
1	52	ALA	ALA	G	G	1 - 28	2 - 29
2	52	ALA	ALA	H	H	1 - 28	2 - 29
1	53	ALA	ALA	G	G	1 - 28	2 - 29
2	53	ALA	ALA	I	I	1 - 28	2 - 29
1	54	ALA	ALA	G	G	1 - 28	2 - 29
2	54	ALA	ALA	J	J	1 - 28	2 - 29
1	55	ALA	ALA	G	G	1 - 28	2 - 29
2	55	ALA	ALA	K	K	1 - 28	2 - 29
1	56	ALA	ALA	G	G	1 - 28	2 - 29
2	56	ALA	ALA	L	L	1 - 28	2 - 29
1	57	GLY	GLY	H	H	1 - 30	2 - 31
2	57	GLY	GLY	I	I	1 - 30	2 - 31
1	58	GLY	GLY	H	H	1 - 30	2 - 31
2	58	GLY	GLY	J	J	1 - 30	2 - 31
1	59	GLY	GLY	H	H	1 - 30	2 - 31
2	59	GLY	GLY	K	K	1 - 30	2 - 31
1	60	GLY	GLY	H	H	1 - 30	2 - 31
2	60	GLY	GLY	L	L	1 - 30	2 - 31
1	61	GLY	GLY	I	I	1 - 30	2 - 31
2	61	GLY	GLY	J	J	1 - 30	2 - 31
1	62	GLY	GLY	I	I	1 - 30	2 - 31
2	62	GLY	GLY	K	K	1 - 30	2 - 31
1	63	GLY	GLY	I	I	1 - 30	2 - 31
2	63	GLY	GLY	L	L	1 - 30	2 - 31
1	64	GLY	GLY	J	J	1 - 30	2 - 31
2	64	GLY	GLY	K	K	1 - 30	2 - 31
1	65	GLY	GLY	J	J	1 - 30	2 - 31
2	65	GLY	GLY	L	L	1 - 30	2 - 31
1	66	GLY	GLY	K	K	1 - 30	2 - 31
2	66	GLY	GLY	L	L	1 - 30	2 - 31

NCS ensembles :

#1: Protein/peptide	CC-Hex-L24Nle Mass: 3234.871 Da / Num. of mol.: 12 / Source method: obtained synthetically / Source*: (synth.) synthetic construct (others)
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Chemical	ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE Mass: 88.105 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₈O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 111 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.97 Å³/Da / Density % sol: 58.65 %
Crystal grow	Temperature: 297 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.8 M Ammonium sulfate, 0.05 M MES, 5 % v/v 1,4-Dioxane

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Data collection

Diffraction

Mean temperature: 80 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

Diamond

/ Beamline: I04 / Wavelength: 0.9794 Å

Detector

Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 9, 2014

Radiation

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

Radiation wavelength

Wavelength: 0.9794 Å / Relative weight: 1

Reflection

Resolution: 2→47.92 Å / Num. obs: 32110 / % possible obs: 99.8 % / Redundancy: 9.1 % / B_iso Wilson estimate: 26.502 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.105 / R_pim(I) all: 0.051 / R_rim(I) all: 0.111 / Net I/σ(I): 13

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	% possible all
2-2.05	9.3	1.73	1.5	2340	0.511	0.6	1.833	99.9
8.94-47.92	7.7	0.046	27.2	375	1	0.016	0.049	85.8

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0241	refinement
iMOSFLM		data reduction
Aimless	0.7.1	data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2→45.78 Å / Cor.coef. F_o:F_c: 0.954 / Cor.coef. F_o:F_c free: 0.946 / SU B: 5.283 / SU ML: 0.137 / Cross valid method: THROUGHOUT / ESU R: 0.177 / ESU R Free: 0.162 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.25762	1558	4.9 %	RANDOM
R_work	0.22098	-	-	-
obs	0.22271	30486	99.76 %	-

Solvent computation

Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å

Displacement parameters

B_iso mean: 42.57 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.44 Å²	0 Å²	0 Å²
2-	-	0.92 Å²	-0 Å²
3-	-	-	-3.36 Å²

Refinement step

Cycle: 1 / Resolution: 2→45.78 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2720	0	72	111	2903

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.013	2810
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	3048
X-RAY DIFFRACTION	r_angle_refined_deg	1.41	1.641	3715
X-RAY DIFFRACTION	r_angle_other_deg	1.289	1.585	7081
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.378	5	346
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.027	25.567	97
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.477	15	565
X-RAY DIFFRACTION	r_dihedral_angle_4_deg
X-RAY DIFFRACTION	r_chiral_restr	0.066	0.2	385
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	2924
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	436
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	4.083	3.986	1441
X-RAY DIFFRACTION	r_mcbond_other	4.079	3.982	1439
X-RAY DIFFRACTION	r_mcangle_it	5.528	5.927	1776
X-RAY DIFFRACTION	r_mcangle_other	5.528	5.928	1776
X-RAY DIFFRACTION	r_scbond_it	5.78	4.854	1369
X-RAY DIFFRACTION	r_scbond_other	5.778	4.855	1370
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	9.054	6.878	1940
X-RAY DIFFRACTION	r_long_range_B_refined	10.39	49.592	3179
X-RAY DIFFRACTION	r_long_range_B_other	10.394	49.457	3164
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

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

LS refinement shell

Resolution: 2→2.052 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.352	110	-
R_work	0.329	2224	-
obs	-	-	99.91 %

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