PDB-3vjf: Crystal structure of de novo 4-helix bundle protein WA20

ID or keywords:

Entry

Database: PDB / ID: 3vjf

Title

Crystal structure of de novo 4-helix bundle protein WA20

Components

WA20

Keywords

DE NOVO PROTEIN / PROTEIN DESIGN / BINARY PATTERNED DESIGN / FOUR HELIX BUNDLE / 3D DOMAIN SWAPPING / Rudimentary enzymatic activities

Function / homology

Designed four-helix bundle protein / hypothetical protein mp506/mpn330, domain 1 / Up-down Bundle / Mainly Alpha / :

Function and homology information

Biological species

synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2.2 Å

Authors

Arai, R. / Kimura, A. / Kobayashi, N. / Matsuo, K. / Sato, T. / Wang, A.F. / Platt, J.M. / Bradley, L.H. / Hecht, M.H.

Citation

Journal: J.Phys.Chem.B / Year: 2012
Title: Domain-swapped dimeric structure of a stable and functional de novo four-helix bundle protein, WA20
Authors: Arai, R. / Kobayashi, N. / Kimura, A. / Sato, T. / Matsuo, K. / Wang, A.F. / Platt, J.M. / Bradley, L.H. / Hecht, M.H.

History

Deposition	Oct 18, 2011	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Mar 28, 2012	Provider: repository / Type: Initial release
Revision 1.1	Jul 17, 2013	Group: Database references
Revision 1.2	Nov 22, 2017	Group: Refinement description / Category: software / Item: _software.name
Revision 1.3	Oct 30, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3vjf.cif.gz	98.3 KB	Display	PDBx/mmCIF format
PDB format	pdb3vjf.ent.gz	78.5 KB	Display	PDB format
PDBx/mmJSON format	3vjf.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/vj/3vjf ftp://data.pdbj.org/pub/pdb/validation_reports/vj/3vjf	HTTPS FTP

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Related structure data

Similar structure data	4n3x-d 5vjt-d 5vju-d 6z0c-2 6kos-1 6kos-2 6b87-3 5vjs-d 6lhz-d 5d5z-2 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: WA20

B: WA20

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	65.950, 102.858, 31.344
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	18
Space group name H-M	P2₁2₁2

Components on special symmetry positions

ID	Model	Components
1	1	A-201- K
2	1	A-118- HOH

#1: Protein	WA20 Mass: 12943.274 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: a de novo protein from artificially designed superfamily of 4-helix bundle Source: (gene. exp.) synthetic construct (others) / Plasmid: pET-3a / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)
#2: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 55 / 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: 2.05 Å³/Da / Density % sol: 40.1 % / Mosaicity: 1.338 °
Crystal grow	Temperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 8.2 Details: 1.344M potassium phosphate dibasic, 0.056M sodium phosphate monobasic monohydrate, pH 8.2, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K

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Data collection

Diffraction

Mean temperature: 95 K

Diffraction source

Source:

SYNCHROTRON / Site:

Photon Factory

/ Beamline: BL-5A / Wavelength: 0.97881, 0.97908, 0.90000

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 19, 2010

Radiation

Monochromator: Si(111) double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.97881	1
2	0.97908	1
3	0.9	1

Reflection

Resolution: 2.2→50 Å / Num. obs: 11102 / % possible obs: 97.4 % / Observed criterion σ(I): -3 / Redundancy: 6.1 % / B_iso Wilson estimate: 43.5 Å² / R_merge(I) obs: 0.098 / Χ²: 1.001 / Net I/σ(I): 11.6

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique all	Χ²	% possible all
2.2-2.28	5.5	0.306	5.4	945	1.037	85.3
2.28-2.37	5.6	0.247	6.5	1009	1.039	91.6
2.37-2.48	6	0.221	7.6	1072	1.013	97.5
2.48-2.61	6.2	0.165	10.7	1152	1.008	100
2.61-2.77	6.5	0.152	11.2	1100	0.987	99.9
2.77-2.99	6.5	0.117	13.1	1123	0.988	100
2.99-3.29	6.5	0.106	13.3	1136	1.009	100
3.29-3.76	6.4	0.078	15	1151	0.953	100
3.76-4.74	6.2	0.079	14.5	1171	0.97	100
4.74-50	5.8	0.093	9.6	1243	1.03	98.7

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Phasing

Phasing

Method:

MAD

Phasing set

ID
1
2
3

Phasing MAD set

Clust-ID	Expt-ID	Set-ID	Wavelength (Å)	F double prime refined	F prime refined
3 wavelength	1	1	0.9788	6.38	-6.89
3 wavelength	1	2	0.9791	3.97	-9.77
3 wavelength	1	3	0.9	3.21	-2.98

Phasing dm

FOM : 0.76 / FOM acentric: 0.77 / FOM centric: 0.7 / Reflection: 10971 / Reflection acentric: 9219 / Reflection centric: 1752

Phasing dm shell

Resolution (Å)	FOM	FOM acentric	FOM centric	Reflection	Reflection acentric	Reflection centric
6.3-31.401	0.92	0.95	0.88	540	332	208
3.9-6.3	0.94	0.96	0.88	1553	1198	355
3.1-3.9	0.91	0.93	0.83	1903	1569	334
2.8-3.1	0.81	0.84	0.62	1914	1629	285
2.4-2.8	0.67	0.69	0.52	3307	2893	414
2.2-2.4	0.47	0.48	0.36	1754	1598	156

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
SOLVE	2.13	phasing
RESOLVE	2.13	phasing
REFMAC	refmac_5.5.0109	refinement
PDB_EXTRACT	3.1	data extraction
SERGUI		data collection
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MAD / Resolution: 2.2→50 Å / Cor.coef. F_o:F_c: 0.927 / Cor.coef. F_o:F_c free: 0.909 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 15.056 / SU ML: 0.176 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.232 / Stereochemistry target values: MAXIMUM LIKELIHOOD

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.255	528	4.8 %	RANDOM
R_work	0.233	-	-	-
obs	0.234	11007	96.8 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso max: 139.68 Å² / B_iso mean: 51.239 Å² / B_iso min: 2 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.11 Å²	0 Å²	0 Å²
2-	-	3.6 Å²	0 Å²
3-	-	-	-2.49 Å²

Refinement step

Cycle: LAST / Resolution: 2.2→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1635	0	1	55	1691

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.021	1674
X-RAY DIFFRACTION	r_angle_refined_deg	1.165	1.868	2242
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.707	5	186
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	39.823	26.239	117
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.409	15	321
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.355	15	2
X-RAY DIFFRACTION	r_chiral_restr	0.09	0.2	222
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	1314
X-RAY DIFFRACTION	r_mcbond_it	0.476	1.5	937
X-RAY DIFFRACTION	r_mcangle_it	0.971	2	1502
X-RAY DIFFRACTION	r_scbond_it	1.892	3	737
X-RAY DIFFRACTION	r_scangle_it	2.8	4.5	740

LS refinement shell

Resolution: 2.2→2.26 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.282	35	-
R_work	0.223	652	-
all	-	687	-
obs	-	687	83.88 %

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	27.6216	7.6448	-20.9149	5.6235	-5.715	16.1982	-1.4039	-0.6408	-2.6133	0.1864	-0.3107	-0.4511	1.4945	0.0506	1.7146	0.87	-0.2192	0.1607	0.3629	0.3855	0.683	30.6364	25.629	37.3327
2	24.4505	13.8467	-19.1073	13.9627	-9.9102	23.3843	-0.0305	-1.1865	-1.1502	0.5896	-0.6975	-0.3456	0.5976	1.3064	0.7281	0.264	0.1238	-0.0015	0.1555	0.1659	0.2601	46.3594	34.0138	24.6354
3	11.4389	6.457	-12.883	2.832	-6.1033	18.7952	-0.3392	-0.4807	-0.4802	-0.0538	-0.1647	-0.1088	0.5751	0.73	0.5039	0.1857	0.0333	0.0212	0.3009	0.0565	0.3243	56.6353	41.9306	12.2604
4	16.6173	9.2067	-7.2822	12.9765	-10.2101	15.3387	0.0273	-0.1931	-0.803	0.1263	-0.3639	-0.6032	-0.4393	0.8278	0.3365	0.1265	-0.0182	-0.0004	0.2697	-0.0396	0.1769	63.438	46.289	2.943
5	26.7312	8.3822	-5.4318	3.6497	-1.5096	6.3765	-0.3183	0.7789	-0.9257	-0.1573	0.1636	-0.1436	0.0249	0.0158	0.1548	0.1393	-0.019	0.0099	0.2828	0.0058	0.147	58.2513	47.1984	-6.3731
6	14.092	-3.8551	-11.5261	1.2693	-1.659	20.8494	0.0048	0.2949	0.2393	-0.1783	-0.0511	-0.4104	0.5598	-0.5949	0.0463	0.1617	-0.0461	0.0138	0.2291	0.0442	0.2436	48.7803	43.8285	2.8019
7	13.2757	3.1988	-12.6869	1.1298	-4.6949	16.5575	-0.2072	0.8674	-0.0366	-0.017	0.2466	0.0822	0.0556	-1.1278	-0.0394	0.1726	-0.0778	-0.0207	0.2433	-0.0487	0.1732	37.0998	41.4247	15.9061
8	27.5619	-8.2684	-17.078	2.5127	2.0388	12.6256	0.3499	1.3221	0.36	-1.0431	0.0021	0.3374	0.3335	-1.2213	-0.3519	0.393	0.0038	-0.1496	0.3504	0.0479	0.1694	26.2727	41.5681	28.8382
9	25.9236	-3.9927	-7.8002	13.5417	-0.4144	9.5788	0.0294	-0.8823	0.3989	0.9027	0.2754	0.521	-0.3777	0.015	-0.3048	0.1772	-0.0122	0.0442	0.2203	0.031	0.1803	19.7467	42.0146	39.0644
10	27.5608	15.8692	-26.897	14.7007	-13.4271	30.7429	-1.0242	0.0735	-1.9019	-0.0396	-0.633	-1.1708	2.6776	0.5843	1.6572	0.6095	0.2231	-0.0187	0.1788	-0.2428	0.5803	50.9041	33.09	7.4887
11	24.3101	-1.0574	-15.0135	11.1144	2.8106	12.3366	-0.438	0.3371	-0.6758	-0.478	0.0436	-0.0765	1.0251	-0.5216	0.3944	0.469	-0.1986	0.0136	0.1998	-0.0261	0.4136	33.9538	30.8334	21.8784
12	32.6733	-7.298	-29.6389	34.7851	-15.8059	36.5383	-0.5243	1.2934	-0.7093	-1.0091	0.1431	-0.1035	1.3796	-1.319	0.3812	0.3968	-0.2973	-0.0844	0.2897	-0.0353	0.1819	21.4631	30.3706	32.721
13	19.0098	-0.3314	-7.1066	5.886	3.7453	-2.3741	-1.6801	-0.2675	-1.6397	0.2397	0.5398	0.1309	-0.3619	-0.6434	1.1403	0.4379	-0.2105	0.0836	0.5807	0.1453	0.6787	16.0832	31.3706	42.873
14	39.4016	15.4023	-3.2351	14.6127	-22.7285	54.6789	0.3381	-1.9657	-1.2026	0.5042	0.1949	0.5689	3.2062	-0.769	-0.533	0.5334	-0.0604	0.1206	0.3838	0.1749	0.1983	24.6081	34.3885	46.5188
15	11.566	3.129	-10.9407	5.0872	-3.9905	14.7831	-0.0091	-0.6527	-0.305	0.2186	-0.0569	0.3347	-0.0026	0.1981	0.0659	0.1643	-0.0547	0.003	0.2822	0.0368	0.1724	32.7648	38.4446	36.9604
16	7.675	3.5732	-7.7072	2.0898	-2.5565	11.4113	0.2186	-0.2477	0.3634	0.0809	-0.0406	0.2212	-0.3834	0.0809	-0.178	0.181	-0.0362	-0.0154	0.1874	0.0048	0.1686	42.4927	44.5156	23.2966
17	13.9087	6.3717	-10.713	11.4938	-12.0021	21.6724	0.0159	-0.1422	0.2605	0.4577	-0.0426	0.5035	-0.6666	0.1721	0.0267	0.1469	0.0016	0.0332	0.1744	-0.0281	0.1576	50.8629	50.7167	12.5525
18	20.6767	0.2911	-12.447	18.2927	-4.3646	21.6151	0.1539	0.6427	0.8788	-0.1404	0.3504	0.2819	-1.044	-0.0979	-0.5043	0.1895	-0.0892	-0.0307	0.2255	0.0383	0.155	54.8099	54.9596	3.5094

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	3 - 18
2	X-RAY DIFFRACTION	2	A	19 - 32
3	X-RAY DIFFRACTION	3	A	33 - 41
4	X-RAY DIFFRACTION	4	A	42 - 49
5	X-RAY DIFFRACTION	5	A	50 - 62
6	X-RAY DIFFRACTION	6	A	63 - 69
7	X-RAY DIFFRACTION	7	A	70 - 85
8	X-RAY DIFFRACTION	8	A	86 - 92
9	X-RAY DIFFRACTION	9	A	93 - 101
10	X-RAY DIFFRACTION	10	B	5 - 22
11	X-RAY DIFFRACTION	11	B	23 - 34
12	X-RAY DIFFRACTION	12	B	35 - 43
13	X-RAY DIFFRACTION	13	B	44 - 56
14	X-RAY DIFFRACTION	14	B	57 - 64
15	X-RAY DIFFRACTION	15	B	65 - 74
16	X-RAY DIFFRACTION	16	B	75 - 87
17	X-RAY DIFFRACTION	17	B	88 - 95
18	X-RAY DIFFRACTION	18	B	96 - 101

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