PDB-5eil: Computational design of a high-affinity metalloprotein homotrimer...

ID or keywords:

Entry

Database: PDB / ID: 5eil

Title

Computational design of a high-affinity metalloprotein homotrimer containing a metal chelating non-canonical amino acid

Components

TRI-05

Keywords

DE NOVO PROTEIN / design / BPY / non canonical aminoacid

Function / homology

Ankyrin repeat-containing domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha / :

Function and homology information

Biological species

synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 2.25 Å

Authors

Sankaran, B. / Zwart, P.H. / Mills, J.H. / Pereira, J.H. / Baker, D.

Funding support

United States, 1items

Citation

Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2016
Title: Computational design of a homotrimeric metalloprotein with a trisbipyridyl core.
Authors: Mills, J.H. / Sheffler, W. / Ener, M.E. / Almhjell, P.J. / Oberdorfer, G. / Pereira, J.H. / Parmeggiani, F. / Sankaran, B. / Zwart, P.H. / Baker, D.

History

Deposition	Oct 30, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 16, 2016	Provider: repository / Type: Initial release
Revision 1.1	Jan 18, 2017	Group: Database references
Revision 1.2	Sep 27, 2017	Group: Author supporting evidence / Refinement description / Category: pdbx_audit_support / software Item: _pdbx_audit_support.funding_organization / _software.classification
Revision 1.3	Dec 25, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0	Nov 15, 2023	Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / database_2 / pdbx_validate_close_contact / struct_conn Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_validate_close_contact.auth_atom_id_2 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5eil.cif.gz	273.6 KB	Display	PDBx/mmCIF format
PDB format	pdb5eil.ent.gz	229.7 KB	Display	PDB format
PDBx/mmJSON format	5eil.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5eil_validation.pdf.gz	442.5 KB	Display	wwPDB validaton report
Full document	5eil_full_validation.pdf.gz	445.6 KB	Display
Data in XML	5eil_validation.xml.gz	20 KB	Display
Data in CIF	5eil_validation.cif.gz	26.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ei/5eil ftp://data.pdbj.org/pub/pdb/validation_reports/ei/5eil	HTTPS FTP

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Related structure data

Similar structure data	2qm4-2 3sr2-3 1x90-4 1hix-1 1x90-3 2xpj-d 1q89-2 6kxk-3 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: TRI-05

B: TRI-05

C: TRI-05

hetero molecules

51 kDa, 3 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)	63.107, 63.940, 64.831
Angle α, β, γ (deg.)	90.00, 116.87, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	TRI-05 Mass: 16977.205 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Chemical	ChemComp-FE / FE (III) ION Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 105 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.29 Å³/Da / Density % sol: 46.37 %
Crystal grow	Temperature: 294 K / Method: vapor diffusion, sitting drop Details: 0.1 M Magnesium Chloride, 0.1 M Sodium Acetate trihydrate pH 4.5 and 30% Pentaerythritol propoxylate (5/4 PO/OH)

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 11, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.25→28.92 Å / Num. obs: 22017 / % possible obs: 100 % / Redundancy: 7.7 % / R_merge(I) obs: 0.28 / Net I/σ(I): 13.92

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Processing

Software

Name	Version	Classification
PHENIX	dev_1839	refinement
xia2		data scaling
XDS		data scaling
PHASER		phasing

Refinement

Resolution: 2.25→28.92 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.43 / Phase error: 29.33 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.245	2202	10.02 %
R_work	0.2138	-	-
obs	0.2169	21968	99.72 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.25→28.92 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3568	0	1	105	3674

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	3650
X-RAY DIFFRACTION	f_angle_d	0.769	4920
X-RAY DIFFRACTION	f_dihedral_angle_d	11.785	1383
X-RAY DIFFRACTION	f_chiral_restr	0.028	559
X-RAY DIFFRACTION	f_plane_restr	0.004	651

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.249-2.2979	0.534	143	0.4768	1177	X-RAY DIFFRACTION	97
2.2979-2.3513	0.4426	118	0.3554	1212	X-RAY DIFFRACTION	99
2.3513-2.4101	0.3121	143	0.282	1229	X-RAY DIFFRACTION	100
2.4101-2.4752	0.3089	132	0.2777	1244	X-RAY DIFFRACTION	100
2.4752-2.548	0.3027	152	0.265	1211	X-RAY DIFFRACTION	100
2.548-2.6302	0.3001	126	0.2609	1258	X-RAY DIFFRACTION	100
2.6302-2.7241	0.2821	134	0.2509	1229	X-RAY DIFFRACTION	100
2.7241-2.8331	0.2746	136	0.2547	1227	X-RAY DIFFRACTION	100
2.8331-2.9619	0.2853	143	0.2456	1236	X-RAY DIFFRACTION	100
2.9619-3.1179	0.2646	138	0.2408	1225	X-RAY DIFFRACTION	100
3.1179-3.313	0.2073	142	0.2314	1253	X-RAY DIFFRACTION	100
3.313-3.5685	0.2769	136	0.2064	1236	X-RAY DIFFRACTION	100
3.5685-3.9268	0.188	122	0.1749	1259	X-RAY DIFFRACTION	100
3.9268-4.4934	0.2026	147	0.1716	1243	X-RAY DIFFRACTION	100
4.4934-5.6547	0.2153	141	0.1799	1247	X-RAY DIFFRACTION	100
5.6547-29.6607	0.197	149	0.1648	1280	X-RAY DIFFRACTION	100

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	7.4609	2.9513	-1.3969	1.9304	0.2515	9.1759	0.0479	0.6526	0.8227	-0.8296	-0.1686	0.2205	-1.035	-0.6168	0.3052	0.4106	0.0972	-0.0533	0.4008	-0.0012	0.3744	24.7558	39.661	7.5358
2	2.9631	-2.9037	0.8394	7.4344	1.1575	6.9661	0.0865	-0.7967	-0.6345	0.2277	-0.2194	2.0042	0.3807	-1.4014	0.0649	0.3203	-0.0256	-0.0018	0.6187	-0.0587	0.576	18.1447	33.4449	13.7781
3	2.8438	-1.5055	3.4034	6.5596	0.2346	4.9034	-0.3999	-0.3703	0.9594	-1.1676	0.3879	-0.5101	-1.7811	0.9998	-0.1197	0.7192	-0.0976	-0.0953	0.4618	-0.1702	0.7692	19.5729	42.175	2.1187
4	5.7621	1.1342	-1.0351	4.7074	-2.4767	7.4487	0.1492	-0.5044	0.7273	-0.6108	-0.3744	-0.2116	0.1322	0.6452	0.0298	0.3578	0.0224	-0.0573	0.3012	-0.0682	0.4074	20.0631	30.9163	-0.2708
5	9.2243	-3.441	1.7858	6.5751	-0.9935	8.6202	0.3373	-0.9263	-0.6704	0.6103	-0.0319	1.8494	1.0178	-1.4615	-0.2855	0.4263	-0.0834	-0.0148	0.4814	-0.0618	0.5112	12.6773	29.8442	6.195
6	4.0202	-1.2438	0.8841	8.4804	-1.0101	5.5169	-0.3207	0.8003	1.197	-0.3471	-0.0325	0.1416	-1.0197	-0.0693	0.4855	0.7121	-0.0495	-0.3142	0.3465	0.0514	0.6667	15.8108	37.8008	-7.4748
7	4.0847	-5.5656	1.7909	9.4512	1.6252	8.4715	-0.1569	-0.1185	-0.3692	-0.0585	-0.2053	0.2557	0.1509	-0.5924	0.329	0.3101	-0.0655	-0.0563	0.2428	-0.0275	0.3591	14.5735	26.1026	-5.7242
8	10.1986	-0.4596	-4.8538	4.8321	2.6018	4.4665	0.6461	0.5409	-0.0439	-1.2664	-0.7771	1.0618	-1.7959	-0.5116	0.1068	0.7897	0.0923	-0.3024	0.4465	0.0469	0.7321	13.2234	33.3454	-14.577
9	7.9932	-6.1386	3.6938	6.5333	-4.605	6.745	-0.3334	0.4547	1.3656	-0.2047	-0.1227	-1.2233	-0.3233	0.1272	0.4211	0.3706	0.0314	-0.0186	0.2992	0.0867	0.4017	18.5386	24.0672	-15.6585
10	8.7183	1.65	1.3783	2.1109	3.0498	5.1202	0.0343	-0.4841	-0.6715	0.0773	-0.0809	0.7675	1.6427	-1.9538	0.1496	0.4353	-0.1433	0.0326	0.4757	-0.038	0.4754	10.1053	19.1681	-12.5845
11	7.1172	1.2125	-1.6582	6.9375	-0.6033	8.4779	0.3793	0.8126	0.2572	-1.2069	-0.476	0.5528	-0.8095	0.0833	-0.0362	0.7135	0.0576	-0.1763	0.5687	0.0934	0.5081	13.2823	28.837	-23.0316
12	4.5302	-3.4901	-6.2239	3.1294	5.1368	8.7103	0.1643	-0.0642	0.398	-1.5601	0.0926	-0.6931	-0.347	1.224	-0.1317	0.6055	0.0868	0.0183	0.568	0.0535	0.4863	20.5009	20.6378	-23.7216
13	9.676	1.6763	4.3655	5.7656	1.6997	4.084	0.1528	0.8972	-1.7153	-0.2889	0.0624	0.7661	1.1352	-0.4423	-0.1436	0.8184	-0.1259	0.0154	0.5951	-0.0402	0.6223	12.648	14.6371	-22.3568
14	9.801	-1.454	0.0067	8.6304	0.4574	5.7138	0.278	1.3553	-0.0608	-0.9311	-0.1896	-0.1042	-0.0724	-0.0993	-0.1019	0.3201	0.076	-0.0423	0.523	-0.0027	0.2836	33.5333	33.1541	2.5551
15	7.8334	2.5439	2.2928	5.9588	-0.0251	2.5214	0.0355	0.5394	0.7963	0.172	-0.0216	0.0043	-0.614	-0.3575	-0.1364	0.3596	0.1174	0.0848	0.3382	0.0491	0.2803	42.2386	33.9557	4.4252
16	8.4343	0.9528	0.3706	5.7417	-0.547	6.2711	0.2296	0.8319	-0.6286	-0.5877	-0.0716	-0.7645	0.1679	0.2963	-0.1588	0.3672	0.146	0.0238	0.2741	-0.0229	0.3246	46.8272	29.0189	2.6444
17	5.1606	1.2117	-2.0232	5.9961	-2.9862	5.2107	0.2553	0.2751	-0.6785	-0.709	-0.2364	0.1173	0.7039	0.0408	-0.043	0.3839	0.0896	-0.0736	0.294	-0.0065	0.3004	49.9538	22.6489	8.6277
18	9.3432	-3.2845	2.9221	8.4096	-4.7076	8.9071	-0.052	0.1255	0.3341	0.0391	-0.0976	-0.5609	0.0667	0.7871	0.0969	0.2489	0.0727	0.0315	0.3811	-0.0292	0.3016	60.8554	22.7223	16.0163
19	9.4509	-1.5219	-1.3374	7.7177	-4.3387	5.4094	0.3237	-1.1835	1.1919	0.7304	-0.4633	0.0936	-0.8431	-0.1818	0.1335	0.3349	-0.0018	0.0206	0.4463	-0.1428	0.3404	32.8446	39.3664	15.5789
20	5.3265	-0.3337	-2.0491	5.408	4.4935	7.9803	0.2222	-0.2987	0.1342	0.1554	0.1914	-0.0447	0.4094	0.1488	-0.4061	0.3208	-0.0639	-0.0118	0.3236	0.0137	0.2653	31.998	36.5929	21.2402
21	6.1604	1.0823	-4.0775	8.6133	3.3534	4.9174	0.4133	-0.6497	-2.3718	1.6825	0.363	-0.9521	2.6642	0.0321	-0.1126	0.7019	-0.2036	-0.1809	0.4617	0.1578	0.695	31.945	29.8037	28.1425
22	8.2537	-3.948	3.5107	5.5407	-0.8298	4.3228	0.305	-1.1351	0.4981	-0.2181	0.0178	-0.0744	0.3244	-0.9096	-0.3702	0.3918	-0.1627	0.0817	0.5013	-0.0513	0.354	24.3018	44.1688	29.2526
23	8.2867	-0.321	-0.6502	2.6221	3.8162	5.408	0.07	-1.0257	-1.1747	0.3848	0.1859	0.1346	0.5923	-0.443	-0.2041	0.4262	-0.2227	0.0534	0.6758	0.1073	0.4248	19.9652	33.2626	31.0894
24	7.4177	-2.7206	0.8219	5.6883	-0.19	4.824	-0.2648	-2.0452	1.159	0.6699	0.5048	-0.695	-0.5379	-0.8507	-0.2091	0.5406	-0.0013	0.0034	0.9901	-0.2942	0.5485	17.5977	43.9255	34.842
25	2.67	-1.2524	1.3636	7.43	4.0178	4.9566	0.13	-0.9604	-0.7612	0.5956	-0.0062	0.8824	-0.3897	0.315	-0.0147	0.4771	-0.2326	0.0976	0.7955	0.1066	0.5534	9.7793	37.3107	31.1858
26	8.0914	-1.8681	7.421	6.5635	2.874	2.0335	0.8024	-2.0625	-1.2292	1.4885	-0.2092	0.7485	1.5173	1.2001	-0.2996	0.7979	-0.1585	0.0925	1.2014	0.3317	0.6692	12.5226	30.5837	38.5087
27	4.7231	-3.8822	3.1643	6.0649	-2.6121	5.5905	-0.2576	-2.2946	0.9359	0.3069	0.4411	-0.2218	0.3315	-1.1806	-0.2377	0.6365	-0.0673	0.1888	1.0035	-0.144	0.5734	8.6464	44.5681	38.2039
28	4.5646	3.2924	0.7891	8.4337	0.3406	2.1045	0.1271	0.9259	0.7279	0.1489	1.0458	1.4326	-0.637	0.3848	-0.8368	0.6393	-0.0567	0.0771	0.9764	0.1608	0.7628	0.9559	38.6522	32.8235
29	5.4959	-2.6004	-2.5335	3.1605	1.3097	5.8069	-0.7351	-1.1855	-1.1325	1.1917	0.5011	1.621	2.0284	-2.2132	0.4897	0.8001	-0.2605	0.2091	1.5776	0.1626	0.9869	2.0222	32.6825	40.7175

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 0 through 13 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 14 through 24 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 25 through 38 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 39 through 48 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 49 through 58 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 59 through 71 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 72 through 90 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 91 through 104 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 105 through 114 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 115 through 123 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 124 through 137 )
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 138 through 147 )
13	X-RAY DIFFRACTION	13	chain 'A' and (resid 148 through 157 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 0 through 24 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 25 through 48 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 49 through 71 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 72 through 90 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 91 through 158 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 0 through 13 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 14 through 48 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 49 through 58 )
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 59 through 71 )
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 72 through 90 )
24	X-RAY DIFFRACTION	24	chain 'C' and (resid 91 through 104 )
25	X-RAY DIFFRACTION	25	chain 'C' and (resid 105 through 114 )
26	X-RAY DIFFRACTION	26	chain 'C' and (resid 115 through 123 )
27	X-RAY DIFFRACTION	27	chain 'C' and (resid 124 through 137 )
28	X-RAY DIFFRACTION	28	chain 'C' and (resid 138 through 147 )
29	X-RAY DIFFRACTION	29	chain 'C' and (resid 148 through 158 )

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About Yorodumi

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Yorodumi