PDB-6q5j: Crystal structure of a CC-Hex mutant that forms a parallel six-he...

ID or keywords:

Entry

Database: PDB / ID: 6q5j

Title

Crystal structure of a CC-Hex mutant that forms a parallel six-helix coiled coil CC-Hex*-L24E

Components

CC-Hex*-L24E

Keywords

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

Biological species

synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.69 Å

Authors

Rhys, G.G. / Wood, C.W. / Beesley, J.L. / 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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PDBx/mmCIF format	6q5j.cif.gz	83.8 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	6q5j_validation.pdf.gz	465.3 KB	Display	wwPDB validaton report
Full document	6q5j_full_validation.pdf.gz	466.2 KB	Display
Data in XML	6q5j_validation.xml.gz	11.3 KB	Display
Data in CIF	6q5j_validation.cif.gz	16.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/q5/6q5j ftp://data.pdbj.org/pub/pdb/validation_reports/q5/6q5j	HTTPS FTP

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Related structure data

Related structure data	6q5hC 6q5iC 6q5kC 6q5lC 6q5mC 6q5nC 6q5oC 6q5pC 6q5qC 6q5rC 6q5sC C: citing same article (ref.)
Similar structure data	3r47-1 4kvv-2 6q5n-2 6q5n-1 6yb2-d 3r48-d 4pna-d 4kvu-1 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-Hex*-L24E

B: CC-Hex*-L24E

C: CC-Hex*-L24E

D: CC-Hex*-L24E

E: CC-Hex*-L24E

F: CC-Hex*-L24E

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: equilibrium centrifugation

Unit cell

Length a, b, c (Å)	55.073, 55.073, 138.940
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	94
Space group name H-M	P4₂2₁2

Components on special symmetry positions

ID	Model	Components
1	1	C-130- HOH

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	GLY	GLY	A	A	1 - 30	2 - 31
2	2	GLY	GLY	C	C	1 - 30	2 - 31
1	3	GLY	GLY	A	A	1 - 30	2 - 31
2	3	GLY	GLY	D	D	1 - 30	2 - 31
1	4	GLU	GLU	A	A	1 - 23	2 - 24
2	4	GLU	GLU	E	E	1 - 23	2 - 24
1	5	LYS	LYS	A	A	1 - 25	2 - 26
2	5	LYS	LYS	F	F	1 - 25	2 - 26
1	6	GLY	GLY	B	B	1 - 30	2 - 31
2	6	GLY	GLY	C	C	1 - 30	2 - 31
1	7	GLY	GLY	B	B	1 - 30	2 - 31
2	7	GLY	GLY	D	D	1 - 30	2 - 31
1	8	GLU	GLU	B	B	1 - 23	2 - 24
2	8	GLU	GLU	E	E	1 - 23	2 - 24
1	9	LYS	LYS	B	B	1 - 25	2 - 26
2	9	LYS	LYS	F	F	1 - 25	2 - 26
1	10	GLY	GLY	C	C	1 - 30	2 - 31
2	10	GLY	GLY	D	D	1 - 30	2 - 31
1	11	GLU	GLU	C	C	1 - 23	2 - 24
2	11	GLU	GLU	E	E	1 - 23	2 - 24
1	12	LYS	LYS	C	C	1 - 25	2 - 26
2	12	LYS	LYS	F	F	1 - 25	2 - 26
1	13	GLU	GLU	D	D	1 - 23	2 - 24
2	13	GLU	GLU	E	E	1 - 23	2 - 24
1	14	LYS	LYS	D	D	1 - 25	2 - 26
2	14	LYS	LYS	F	F	1 - 25	2 - 26
1	15	GLU	GLU	E	E	1 - 23	2 - 24
2	15	GLU	GLU	F	F	1 - 23	2 - 24

NCS ensembles :

ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

#1: Protein/peptide	CC-Hex-L24E Mass: 3250.827 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source*: (synth.) synthetic construct (others)
#2: Chemical	ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₁₃NO₄S / Comment: pH buffer*YM
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 210 / 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: 2.83 Å³/Da / Density % sol: 56.6 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 100 mM NaCl, 50 mM MES buffer and 10% w/v PEG 2000 MME at pH 6.0

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Data collection

Diffraction

Mean temperature: 77 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

Diamond

/ Beamline: I03 / Wavelength: 0.97628 Å

Detector

Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 4, 2018

Radiation

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

Radiation wavelength

Wavelength: 0.97628 Å / Relative weight: 1

Reflection

Resolution: 1.69→46.32 Å / Num. all: 610321 / Num. obs: 24910 / % possible obs: 100 % / Redundancy: 24.5 % / CC_1/2: 1 / R_merge(I) obs: 0.193 / R_rim(I) all: 0.197 / Χ²: 0.039 / Net I/σ(I): 10.6

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
1.69-1.73	24.6	1.154	1809	0.505	0.235	1.178	100
7.56-46.32	19.7	0.041	7200	1	0.011	0.042	99.7

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0230	refinement
DIALS	1.8.5-g9e40d7de	data reduction
Aimless	0.5.32	data scaling
PHASER	2.8.2	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.69→43.19 Å / Cor.coef. F_o:F_c: 0.958 / Cor.coef. F_o:F_c free: 0.946 / SU B: 6.566 / SU ML: 0.103 / Cross valid method: THROUGHOUT / ESU R: 0.113 / ESU R Free: 0.115 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.25792	1209	4.9 %	RANDOM
R_work	0.21609	-	-	-
obs	0.21813	23595	99.77 %	-

Solvent computation

Ion probe radii: 1.1 Å / Shrinkage radii: 1.1 Å / VDW probe radii: 1.4 Å

Displacement parameters

B_iso mean: 28.122 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.1 Å²	0 Å²	0 Å²
2-	-	1.1 Å²	0 Å²
3-	-	-	-2.2 Å²

Refinement step

Cycle: 1 / Resolution: 1.69→43.19 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1309	0	24	210	1543

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.015	1396
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.018	1461
X-RAY DIFFRACTION	r_angle_refined_deg	1.618	1.674	1867
X-RAY DIFFRACTION	r_angle_other_deg	1.138	1.689	3411
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.025	5	176
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.959	26.316	57
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.867	15	296
X-RAY DIFFRACTION	r_dihedral_angle_4_deg
X-RAY DIFFRACTION	r_chiral_restr	0.104	0.2	192
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	1511
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	217
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	3.01	1.806	714
X-RAY DIFFRACTION	r_mcbond_other	2.891	1.801	713
X-RAY DIFFRACTION	r_mcangle_it	3.758	2.645	889
X-RAY DIFFRACTION	r_mcangle_other	3.759	2.649	890
X-RAY DIFFRACTION	r_scbond_it	5.864	2.377	682
X-RAY DIFFRACTION	r_scbond_other	5.855	2.377	682
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	7.765	3.301	978
X-RAY DIFFRACTION	r_long_range_B_refined	8.744	24.337	1720
X-RAY DIFFRACTION	r_long_range_B_other	8.503	23.233	1661
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: 1.69→1.734 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.324	72	-
R_work	0.391	1729	-
obs	-	-	99.56 %

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	0.3855	-0.1489	0.8544	0.7352	-1.2496	6.8541	0.0592	0.0074	0.0804	0.0591	0.0259	0.0662	-0.3552	-0.0408	-0.0851	0.0897	-0.0009	0.0174	0.0055	0.0101	0.0477	-15.925	24.777	-21.668
2	0.5272	-0.2296	0.6113	0.8578	-2.1595	7.4798	0.0426	-0.0306	0.1018	0.0048	-0.0953	-0.0587	-0.1745	0.29	0.0527	0.0549	-0.0296	0.0054	0.033	0.0049	0.0364	-7.683	21.597	-21.734
3	0.6381	-0.0462	-1.2675	0.4477	-0.9426	6.2308	0.0232	-0.0664	0.0472	-0.0182	0.0378	-0.0717	0.0422	0.215	-0.061	0.0307	0.0041	0.0081	0.0487	-0.0103	0.0398	-6.022	12.771	-21.995
4	0.7599	0.0003	-1.1983	0.2031	0.6248	6.2111	0.0284	0.004	-0.051	0.0258	0.0584	-0.0272	0.3602	0.0032	-0.0867	0.0714	-0.0064	-0.0027	0.0325	-0.0003	0.0334	-12.431	6.813	-22.444
5	1.2306	0.1957	-0.4055	0.7515	2.099	6.8158	0.0089	0.0082	0.0156	0.0207	-0.0674	0.0558	0.108	-0.1982	0.0585	0.0381	0.0011	-0.0168	0.0358	-0.0011	0.0599	-22.076	10.377	-19.009
6	1.2557	0.549	1.8926	0.2909	0.5253	6.3569	-0.0988	-0.0165	0.0144	-0.0338	0.0351	0.0401	-0.4293	-0.1705	0.0637	0.0634	0.0188	-0.0312	0.0533	0.034	0.0583	-22.887	19.21	-20.221

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	0 - 30
2	X-RAY DIFFRACTION	2	B	1 - 30
3	X-RAY DIFFRACTION	3	C	1 - 30
4	X-RAY DIFFRACTION	4	D	1 - 30
5	X-RAY DIFFRACTION	5	E	1 - 24
6	X-RAY DIFFRACTION	6	F	1 - 26

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