PDB-4yei: Beta1mut synthetic solenoid protein

ID or keywords:

Entry

Database: PDB / ID: 4yei

Title

Beta1mut synthetic solenoid protein

Components

beta1mut

Keywords

STRUCTURAL PROTEIN / solenoid / scaffold

Function / homology

E3 ubiquitin-protein ligase SopA / Pectate Lyase C-like / 3 Solenoid / Mainly Beta

Function and homology information

Biological species

synthetic construct (others)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 3.55 Å

Authors

Murray, J.W. / Kraatz, S.

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Synthetic beta-solenoid proteins with the fragment-free computational design of a beta-hairpin extension.
Authors: MacDonald, J.T. / Kabasakal, B.V. / Godding, D. / Kraatz, S. / Henderson, L. / Barber, J. / Freemont, P.S. / Murray, J.W.

History

Deposition	Feb 24, 2015	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Mar 9, 2016	Provider: repository / Type: Initial release
Revision 1.1	Oct 12, 2016	Group: Database references
Revision 1.2	May 8, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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	4yei.cif.gz	252.6 KB	Display	PDBx/mmCIF format
PDB format	pdb4yei.ent.gz	211.3 KB	Display	PDB format
PDBx/mmJSON format	4yei.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	4yei_validation.pdf.gz	433 KB	Display	wwPDB validaton report
Full document	4yei_full_validation.pdf.gz	434.6 KB	Display
Data in XML	4yei_validation.xml.gz	22.3 KB	Display
Data in CIF	4yei_validation.cif.gz	30.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ye/4yei ftp://data.pdbj.org/pub/pdb/validation_reports/ye/4yei	HTTPS FTP

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Related structure data

Related structure data	4yc5C 4ycqC 4ydtC 4yfoC 5di5C 5dn0C 5dnsC 5dqaC 5draC 5dzbC C: citing same article (ref.)
Similar structure data	4yc5-d 4gzr-2 3ncw-3 5hjb-d 3f42-d 1joy-d 5zi8-d 6mci-d Search similar-shape structures by Omokage search (details) 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

Deposited unit

A: beta1mut

B: beta1mut

C: beta1mut

73.9 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: beta1mut

defined by software
24.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: beta1mut

defined by software
24.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: beta1mut

defined by software
24.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	110.360, 115.960, 164.120
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	23
Space group name H-M	I222

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
1	2	A
2	2	C
1	3	B
2	3	C

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: 20 - 234 / Label seq-ID: 20 - 234

Dom-ID	Ens-ID	Auth asym-ID	Label asym-ID
1	1	A	A
2	1	B	B
1	2	A	A
2	2	C	C
1	3	B	B
2	3	C	C

NCS ensembles :

ID
1
2
3

#1: Protein	beta1mut Mass: 24628.980 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli K-12 (bacteria) / Variant (production host): KRX

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 3.55 Å³/Da / Density % sol: 65.38 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 80 mM MES pH 6.5, 128 mM magnesium sulfate. / PH range: 6.5

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54187 Å
Detector	Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Jul 29, 2011
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.54187 Å / Relative weight: 1
Reflection	Resolution: 3.55→37.43 Å / Num. all: 12716 / Num. obs: 12716 / % possible obs: 98.03 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.66 % / R_merge(I) obs: 0.16 / Net I/av σ(I): 10.631 / Net I/σ(I): 4.8321
Reflection shell	Resolution: 3.55→3.65 Å / Redundancy: 4.69 % / R_merge(I) obs: 1.03 / Mean I/σ(I) obs: 2.08 / % possible all: 97.98

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0103	refinement
xia2		data reduction
xia2		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 3.55→37.43 Å / Cor.coef. F_o:F_c: 0.945 / Cor.coef. F_o:F_c free: 0.936 / SU B: 81.918 / SU ML: 0.516 / Cross valid method: THROUGHOUT / ESU R Free: 0.561 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.24494	623	4.9 %	RANDOM
R_work	0.21838	-	-	-
obs	0.21967	12093	97.54 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 105.716 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.46 Å²	-0 Å²	0 Å²
2-	-	0.16 Å²	-0 Å²
3-	-	-	1.3 Å²

Refinement step

Cycle: 1 / Resolution: 3.55→37.43 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4746	0	0	0	4746

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.016	0.019	4821
X-RAY DIFFRACTION	r_bond_other_d	0.007	0.02	4557
X-RAY DIFFRACTION	r_angle_refined_deg	1.617	1.936	6558
X-RAY DIFFRACTION	r_angle_other_deg	1.265	3	10347
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.649	5	648
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.354	25.647	255
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.792	15	741
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.376	15	33
X-RAY DIFFRACTION	r_chiral_restr	0.096	0.2	768
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	5904
X-RAY DIFFRACTION	r_gen_planes_other	0.005	0.02	1161
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	0.235	0.943	2592
X-RAY DIFFRACTION	r_mcbond_other	0.235	0.942	2591
X-RAY DIFFRACTION	r_mcangle_it	0.414	1.414	3240
X-RAY DIFFRACTION	r_mcangle_other	0.414	1.414	3241
X-RAY DIFFRACTION	r_scbond_it	0.415	0.99	2229
X-RAY DIFFRACTION	r_scbond_other	0.415	0.99	2230
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	0.715	1.467	3319
X-RAY DIFFRACTION	r_long_range_B_refined	2.215	9.09	21409
X-RAY DIFFRACTION	r_long_range_B_other	2.215	9.09	21410
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

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	26374	0.04
1	2	B	26374	0.04
2	1	A	26448	0.04
2	2	C	26448	0.04
3	1	B	26584	0.02
3	2	C	26584	0.02

LS refinement shell

Resolution: 3.554→3.645 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.336	56	-
R_work	0.341	853	-
obs	-	-	97.64 %

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	14.7827	7.2354	-9.4649	5.4339	-2.0833	9.6005	-0.2736	-0.0229	-0.5638	-0.1052	-0.5178	0.1394	0.5335	-0.3851	0.7915	1.8891	0.1282	0.2067	1.4804	-0.7757	1.1508	-3.817	-37.494	-42.13
2	107.0112	8.3451	76.1978	2.4694	5.445	54.4746	-1.1911	2.3661	0.8663	-1.0243	0.116	-0.7624	-0.3325	1.5535	1.0751	2.0624	-0.021	0.498	0.7071	-0.8043	1.6034	-5.626	-40.491	-31.86
3	1.4466	-2.3743	1.3708	10.895	-10.0941	11.8005	1.1763	0.9301	-0.8845	-3.5045	-0.95	0.0232	2.6863	0.2809	-0.2263	2.2141	0.2859	0.0196	1.3343	-1.2723	1.8597	-3.501	-32.651	-34.833
4	9.3164	1.8337	0.3437	9.5381	-1.5705	14.9126	-0.08	0.9834	-1.0742	-0.5682	0.3672	-0.6368	1.2397	-0.101	-0.2871	1.4238	0.0827	0.1614	0.7832	-0.8483	0.9952	-3.189	-30.063	-30.905
5	7.474	1.4802	-0.764	8.1182	3.2234	9.2882	0.0161	1.147	-1.4396	-0.1363	-0.1746	-0.1778	1.1068	-0.2311	0.1584	1.1169	-0.0387	0.1824	0.7178	-0.6963	0.9206	-5.922	-23.085	-21.353
6	15.3957	3.2251	16.533	30.4515	-20.3851	37.1387	2.0362	1.7729	-2.0312	0.8195	-0.5474	-1.4036	1.2394	2.4205	-1.4888	1.7346	0.5883	0.1187	0.7187	-0.6449	1.153	-0.96	-16.653	-11.254
7	22.0864	-8.8599	-5.5059	12.1916	-13.0819	33.5931	0.4628	1.906	-2.769	0.1176	-0.2915	0.4618	-0.4853	-0.2154	-0.1713	1.1219	-0.0096	-0.0508	0.4403	-0.716	1.1836	-9.436	-13.248	-12.375
8	13.0374	0.3113	1.5411	20.1041	-1.201	11.3956	0.0142	0.4206	-0.5202	0.1725	-0.3008	-0.5877	-0.7828	-0.2732	0.2866	0.9231	0.0435	0.0509	0.4246	-0.3645	0.3613	-7.092	-8.187	-7.722
9	45.1862	2.1517	-14.3806	19.1813	9.1615	9.8515	0.4871	0.4838	0.5665	0.9273	-1.8167	2.5778	0.3207	-1.04	1.3296	0.7852	0.1064	-0.0004	0.5032	-0.1212	0.7738	-16.349	-3.392	-5.064
10	41.26	-21.7209	11.4229	18.0264	-11.1139	7.1169	1.7193	-0.8363	-1.0352	0.6486	-0.9267	1.2679	-0.6942	0.7955	-0.7926	1.447	-0.1026	0.2058	0.5782	-0.3923	0.4905	-10.272	-2.147	5.166
11	23.4315	6.9217	6.5069	15.4534	4.9613	2.5243	-0.4098	0.4212	-0.049	-0.9079	0.4037	0.4034	-0.0883	0.1172	0.0061	1.7239	-0.3403	-0.224	1.1252	-0.4264	1.4436	-42.937	-37.746	-41.657
12	26.6887	-27.3812	28.7484	74.798	-56.0256	61.9323	0.0995	1.1939	-2.9146	-2.1244	2.3756	1.3056	1.8725	-0.8498	-2.4751	1.621	-0.1568	0.2096	1.1569	-1.2516	1.5954	-33.469	-32.492	-42.355
13	19.2297	-3.664	2.1126	4.7669	-4.1963	8.7741	-0.3742	0.8802	-1.0798	-0.3989	-0.0219	-0.0263	0.5061	-0.1203	0.3961	1.6767	-0.1805	-0.1899	0.7169	-0.8359	1.0911	-40.632	-30.044	-38.17
14	16.5969	-3.5976	0.6099	6.7832	-0.2397	13.3758	-0.2547	0.3075	-0.4216	-0.8574	-0.1489	0.1705	0.3961	-0.4794	0.4036	1.3027	-0.1728	-0.0574	0.5478	-0.6991	0.9666	-39.456	-25.833	-36.404
15	7.2003	0.083	0.3171	10.1462	2.4516	7.4806	-0.118	0.6634	-0.608	-0.8765	-0.3042	0.1439	0.4375	-0.3057	0.4222	1.0566	-0.0003	-0.2125	0.6331	-0.486	0.7651	-35.121	-17.058	-29.221
16	53.0181	-10.0699	-23.2055	22.2784	-1.8676	24.2515	-0.3178	1.3408	1.0838	-1.4835	0.8175	-0.2363	0.0803	-1.4854	-0.4997	1.1302	-0.1283	-0.2165	0.6916	-0.4759	0.5374	-34.158	-4.223	-27.691
17	19.1449	3.6389	-0.1039	8.3661	-2.5367	17.5053	-0.0197	-0.0458	-0.2903	-0.7897	-0.2379	0.8465	0.5672	0.3236	0.2576	0.9765	-0.001	-0.1719	0.3583	-0.4566	0.6997	-32.236	-7.805	-19.434
18	11.1851	-0.3743	-2.6556	12.1988	-1.4242	14.8474	0.0188	0.5883	-0.0301	0.2298	-0.4271	0.6058	-0.4935	-0.5197	0.4083	0.8652	-0.0241	-0.2181	0.337	-0.3462	0.5896	-32.901	-0.912	-17.241
19	6.9466	-8.7036	5.0354	18.6587	1.9982	12.5652	0.0945	-0.4534	0.2031	1.2524	1.1617	-1.4785	1.5864	0.3206	-1.2562	1.143	-0.046	0.118	0.4825	-0.4047	1.2829	-28.716	-1.491	-7.346
20	7.3473	12.857	4.3917	29.4608	16.5841	30.7263	-1.1308	-0.7839	0.2747	-0.9128	-0.1838	-1.5965	0.0443	0.38	1.3147	1.1813	0.0698	-0.378	0.6733	-0.4469	1.576	-25.582	9.658	-10.355
21	1.2174	-3.3032	0.9665	12.6351	-0.2917	2.3954	-0.0316	-0.1141	-0.2846	-0.1713	0.5559	-0.292	-0.2697	-0.2458	-0.5243	1.9895	0.2738	0.0417	1.2861	-0.3857	1.6643	-24.078	-59.322	-11.657
22	161.7182	12.5814	-151.8393	2.3625	-10.8895	144.3236	-1.9278	-1.6949	-2.2953	-0.0314	-0.3506	1.0695	3.8744	2.0622	2.2785	3.8357	0.6323	-0.719	0.9229	-1.022	1.9998	-31.845	-52.525	-15.002
23	13.1086	-0.9688	2.5009	4.8877	-8.2287	17.3022	0.4554	0.3391	-1.6782	-0.5549	-0.7192	0.0091	0.8331	0.4632	0.2638	2.1912	0.0929	0.1548	0.4253	-0.5357	1.487	-26.673	-51.738	-8.115
24	9.1116	-8.1672	2.8541	9.6337	-6.3061	20.0073	0.357	0.1053	-1.646	-0.8803	-0.4574	0.7004	2.1138	0.1673	0.1004	1.9774	0.0212	-0.0377	0.4486	-0.4572	1.5076	-28.151	-47.732	-6.116
25	7.038	-1.2615	0.638	8.3534	-1.3535	9.1527	0.5774	0.4923	-1.0157	-0.6338	-0.5753	0.6093	2.0833	-0.2833	-0.0021	1.8497	0.0453	0.0544	0.3684	-0.3363	1.0158	-29.657	-36.006	-3.349
26	36.8129	-18.2694	28.7946	20.0393	-15.2103	57.7412	0.7824	-0.6925	-1.385	-0.4724	-1.1119	0.3943	2.9745	-1.6236	0.3295	1.4295	-0.1649	0.2751	0.4358	-0.4249	1.1533	-35.627	-27.77	4.684
27	30.8527	-2.4228	4.6622	10.266	-5.2051	16.4544	-0.6956	0.4342	-1.27	0.1451	0.3776	-0.0694	1.2316	-0.4449	0.3179	1.2983	0.0677	0.1812	0.2567	-0.4361	0.8612	-28.862	-22.892	0.791
28	16.5248	3.6016	7.2141	14.3999	2.6954	18.6312	0.2709	-0.6703	-0.0467	0.3193	-0.3769	0.0068	0.6936	-0.1553	0.106	1.0042	0.0355	0.2328	0.1796	-0.2858	0.6734	-30.524	-18.07	5.963
29	2.55	11.2039	-0.7751	49.7141	-1.7571	5.8472	-0.2745	-0.2631	-0.4843	-1.0764	-0.9608	-1.8115	0.3591	0.7609	1.2353	0.7637	0.0663	-0.0329	0.5755	-0.2289	0.7795	-25.233	-9.384	2.452
30	29.8778	-4.3746	5.2897	69.4367	-5.0979	13.7335	-0.643	0.2952	-0.4885	1.0298	0.6609	0.3515	-0.3405	-0.6582	-0.0179	0.6369	-0.012	0.1171	0.6865	-0.5622	0.5902	-34.604	-4.184	7.77

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	20 - 38
2	X-RAY DIFFRACTION	2	A	39 - 45
3	X-RAY DIFFRACTION	3	A	46 - 61
4	X-RAY DIFFRACTION	4	A	62 - 79
5	X-RAY DIFFRACTION	5	A	80 - 163
6	X-RAY DIFFRACTION	6	A	164 - 171
7	X-RAY DIFFRACTION	7	A	172 - 186
8	X-RAY DIFFRACTION	8	A	187 - 215
9	X-RAY DIFFRACTION	9	A	216 - 224
10	X-RAY DIFFRACTION	10	A	225 - 234
11	X-RAY DIFFRACTION	11	B	20 - 38
12	X-RAY DIFFRACTION	12	B	39 - 45
13	X-RAY DIFFRACTION	13	B	46 - 61
14	X-RAY DIFFRACTION	14	B	62 - 79
15	X-RAY DIFFRACTION	15	B	80 - 163
16	X-RAY DIFFRACTION	16	B	164 - 171
17	X-RAY DIFFRACTION	17	B	172 - 186
18	X-RAY DIFFRACTION	18	B	187 - 215
19	X-RAY DIFFRACTION	19	B	216 - 224
20	X-RAY DIFFRACTION	20	B	225 - 234
21	X-RAY DIFFRACTION	21	C	20 - 38
22	X-RAY DIFFRACTION	22	C	39 - 45
23	X-RAY DIFFRACTION	23	C	46 - 61
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