PDB-5mfg: Designed armadillo repeat protein YIIIM5AII in complex with pepti...

ID or keywords:

Entry

Database: PDB / ID: 5mfg

Title

Designed armadillo repeat protein YIIIM5AII in complex with peptide (RR)4

Components

(RR)4
YIIIM5AII

Keywords

DE NOVO PROTEIN / Designed armadillo repeat protein / peptide binding

Function / homology

Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Alpha Horseshoe / Mainly Alpha

Function and homology information

Biological species

synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.901 Å

Authors

Hansen, S. / Ernst, P. / Reichen, C. / Ewald, C. / Mittl, P. / Plueckthun, A.

Citation

Journal: J. Struct. Biol. / Year: 2018
Title: Curvature of designed armadillo repeat proteins allows modular peptide binding.
Authors: Hansen, S. / Ernst, P. / Konig, S.L.B. / Reichen, C. / Ewald, C. / Nettels, D. / Mittl, P.R.E. / Schuler, B. / Pluckthun, A.

History

Deposition	Nov 18, 2016	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 13, 2017	Provider: repository / Type: Initial release
Revision 1.1	Feb 21, 2018	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2	Jan 17, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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 / _struct_conn.ptnr2_symmetry

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5mfg.cif.gz	583.1 KB	Display	PDBx/mmCIF format
PDB format	pdb5mfg.ent.gz	494.1 KB	Display	PDB format
PDBx/mmJSON format	5mfg.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5mfg_validation.pdf.gz	462.5 KB	Display	wwPDB validaton report
Full document	5mfg_full_validation.pdf.gz	473.1 KB	Display
Data in XML	5mfg_validation.xml.gz	40.5 KB	Display
Data in CIF	5mfg_validation.cif.gz	59.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/mf/5mfg ftp://data.pdbj.org/pub/pdb/validation_reports/mf/5mfg	HTTPS FTP

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Related structure data

Related structure data	5mfbC 5mfeC 5mffC 5mfhC 5mfiC 5mfjC 5mfkC 5mflC 5mfmC 5mfnC 5mfoC 4plsS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5ert-1 3wmt-d 2ws3-1 2ws3-2 5erq-1 2wp9-2 6fgd-1 2wdr-1 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: YIIIM5AII

B: YIIIM5AII

C: YIIIM5AII

D: YIIIM5AII

E: (RR)4

hetero molecules

122 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	168.540, 168.540, 80.580
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	171
Space group name H-M	P6₂

#1: Protein	YIIIM5AII Mass: 30027.445 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli K-12 (bacteria)
#2: Protein/peptide	(RR)4 Mass: 1589.953 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Ca
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 486 / 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: 2.71 Å³/Da / Density % sol: 54.69 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 18.0% PEG 3350, 0.15 M KSCN, 0.1 M Na-Acetate pH5.5

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 7, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.9→48.653 Å / Num. obs: 102534 / % possible obs: 99.9 % / Redundancy: 20.6 % / CC_1/2: 1 / R_merge(I) obs: 0.138 / Net I/σ(I): 19.47
Reflection shell	Resolution: 1.9→1.95 Å / Redundancy: 20.5 % / R_merge(I) obs: 6.14 / CC_1/2: 0.19 / % possible all: 98.3

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Processing

Software

Name	Version	Classification
PHENIX	(1.10_2155: ???)	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4PLS

4pls

Resolution: 1.901→48.653 Å / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 34.04

	R_factor	Num. reflection	% reflection
R_free	0.2133	5053	4.94 %
R_work	0.182	-	-
obs	0.2075	102268	99.83 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 1.901→48.653 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7944	0	13	486	8443

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	8092
X-RAY DIFFRACTION	f_angle_d	0.496	11034
X-RAY DIFFRACTION	f_dihedral_angle_d	14.731	5011
X-RAY DIFFRACTION	f_chiral_restr	0.035	1313
X-RAY DIFFRACTION	f_plane_restr	0.002	1491

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 (%)
1.9021-1.9349	0.3774	227	0.3714	4767	X-RAY DIFFRACTION	94
1.9349-1.97	0.3401	261	0.3254	4844	X-RAY DIFFRACTION	95
1.97-2.0079	0.3695	250	0.3186	4862	X-RAY DIFFRACTION	95
2.0079-2.0489	0.3131	249	0.3043	4797	X-RAY DIFFRACTION	95
2.0489-2.0934	0.333	265	0.2944	4813	X-RAY DIFFRACTION	95
2.0934-2.1421	0.3031	249	0.2841	4849	X-RAY DIFFRACTION	95
2.1421-2.1956	0.2769	235	0.2717	4889	X-RAY DIFFRACTION	95
2.1956-2.2549	0.2918	242	0.2547	4856	X-RAY DIFFRACTION	95
2.2549-2.3213	0.264	250	0.2347	4807	X-RAY DIFFRACTION	95
2.3213-2.3961	0.2372	220	0.2327	4897	X-RAY DIFFRACTION	96
2.3961-2.4817	0.246	240	0.2219	4879	X-RAY DIFFRACTION	95
2.4817-2.581	0.2232	272	0.2103	4803	X-RAY DIFFRACTION	95
2.581-2.6983	0.2312	270	0.1972	4845	X-RAY DIFFRACTION	95
2.6983-2.8404	0.2179	248	0.2063	4869	X-RAY DIFFRACTION	95
2.8404-3.018	0.243	262	0.2004	4871	X-RAY DIFFRACTION	95
3.018-3.2506	0.2219	271	0.1973	4829	X-RAY DIFFRACTION	95
3.2506-3.5769	0.2532	271	0.2077	4869	X-RAY DIFFRACTION	95
3.5769-4.0925	0.224	266	0.1864	4888	X-RAY DIFFRACTION	95
4.0925-5.1486	0.2138	223	0.1677	4933	X-RAY DIFFRACTION	96
5.1486-24.9312	0.222	275	0.1775	4988	X-RAY DIFFRACTION	95

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	0.3837	0.0991	-0.0607	0.0385	0.0556	0.354	-0.0168	-0.1811	-0.0643	0.0608	-0.0169	-0.0065	0.1899	-0.0291	-0	0.3059	0.0045	0.0349	0.2835	-0.005	0.3636	-47.4377	181.0411	9.7759
2	0.0395	0.0098	0.035	0.0062	-0.065	0.0625	-0.1581	-0.2196	-0.2315	-0.0748	0.17	0.1846	0.0124	0.2849	0	0.2517	0.0143	0.0367	0.2512	-0.0205	0.3619	-39.3457	185.1815	6.1816
3	0.5006	-0.1542	-0.4804	0.0677	-0.1428	0.6326	-0.0149	0.0466	-0.0529	-0.0674	-0.0942	0.0569	-0.0083	-0.0711	-0	0.2409	0.0401	-0.0004	0.2336	-0.0633	0.2998	-34.9983	187.8573	-6.1242
4	0.2004	-0.0654	-0.5071	0.2223	0.099	0.3121	0.0713	0.0814	-0.0486	-0.1071	-0.0598	-0.0003	-0.1513	0.0369	0	0.2911	0.0511	0.0146	0.1931	-0.029	0.2377	-23.0133	187.6383	-15.6354
5	0.1728	0.0038	-0.2135	0.2677	0.1146	0.0721	0.0614	0.2194	0.0133	-0.1344	-0.0496	-0.0518	-0.172	0.0782	-0	0.3872	0.0394	0.0465	0.2516	-0.0153	0.2534	-16.2417	186.2184	-23.2025
6	0.0737	0.0047	-0.0394	-0.0114	0.0618	-0.0083	-0.0099	0.0399	0.2651	-0.0502	-0.1676	0.0157	0.1442	0.0834	0	0.3334	0.0254	0.0418	0.256	-0.022	0.2933	-14.767	178.4533	-17.9588
7	0.0828	0.0418	-0.0477	0.0204	-0.0028	-0.0026	-0.0195	0.2153	-0.0336	0.4387	0.1197	0.1978	0.1536	-0.0738	-0	0.4597	-0.0006	0.0318	0.3691	-0.0482	0.3955	-24.1581	168.8618	-21.9849
8	-0.0167	-0.001	-0.0371	0.0383	0.0154	0.0129	-0.0263	0.2348	-0.344	0.3455	0.1543	0.2018	0.2341	-0.2182	0	1.0746	0.0185	-0.0432	0.7296	-0.0822	0.6994	-24.6815	168.1735	-43.5138
9	0.0082	-0.0205	0.0093	-0.0097	0.0262	0.0056	0.0469	0.1655	0.2341	-0.4197	0.0017	0.6387	-0.2017	-0.1087	-0	0.8526	0.0355	-0.0073	1.0094	-0.0252	0.8759	-33.8224	178.639	-47.0333
10	0.3151	-0.0764	-0.3492	0.3878	0.3316	0.365	0.0661	0.0801	-0.0246	-0.1101	-0.0534	-0.0632	-0.0537	0.0397	-0	0.3157	0.0234	0.0432	0.2623	-0.05	0.2711	-9.5251	171.1484	-28.4496
11	0.0663	0.0055	0.1105	0.1713	0.1847	0.2001	0.0779	0.0913	-0.0932	-0.2201	0.0132	0.0053	0.0866	0.1281	-0	0.3208	0.0355	0.0218	0.2594	-0.0717	0.3001	-9.9542	157.8081	-35.9968
12	0.1315	0.1851	0.1354	0.2899	0.2179	0.5609	0.0639	0.0541	-0.0851	-0.2048	0.0112	-0.0332	-0.0309	-0.0355	-0	0.4148	0.0493	-0.0362	0.2924	-0.0805	0.2842	-20.0417	146.5871	-47.439
13	0.0185	0.0418	-0.0012	0.0299	0.0009	0.0125	-0.0099	0.1265	0.1813	-0.2028	0.1601	0.0934	-0.3561	-0.1528	-0	0.7053	0.1369	-0.0902	0.6603	-0.0204	0.4535	-32.4366	148.8707	-54.5105
14	0.0014	0.005	-0.0088	0.0065	0.0266	0.0181	0.0481	-0.0565	-0.1888	-0.018	-0.0222	0.2884	0.0616	-0.1234	-0	0.8744	-0.111	-0.0088	0.8199	-0.1526	0.7148	-31.4861	166.9695	27.5296
15	0.2588	-0.1468	0.0724	0.1703	0.3371	0.182	0.0712	-0.1632	0.0877	0.1466	-0.0934	-0.0612	0.1967	0.1631	0	0.3259	0.0265	0.0057	0.3009	-0.0426	0.2804	-9.7186	173.4966	11.7163
16	0.0177	-0.0015	0.0077	0.0648	0.0608	-0.0075	-0.1056	-0.0683	-0.1431	0.0481	-0	-0.1741	-0.0127	-0.203	-0	0.2974	0.0127	0.0332	0.2544	-0.0267	0.2991	-14.6182	179.472	6.1128
17	0.2771	-0.1833	-0.1149	0.4621	0.558	0.3153	-0.0132	-0	0.0215	0.0833	0.0329	0.0279	0.0141	0.1207	-0	0.2456	0.0162	0.0108	0.262	-0.0438	0.2533	-16.7809	188.3173	16.5485
18	0.5638	0.332	-0.4723	0.3139	-0.0756	0.6623	0.0863	-0.1049	0.1112	0.1269	-0.0671	0.0719	0.001	-0.0717	0	0.2208	-0.0007	0.0419	0.2693	-0.057	0.2576	-31.3967	196.6427	27.5837
19	0.0715	-0.0045	-0.056	0.1283	-0.2345	0.113	0.3828	-0.6298	0.3853	0.2923	-0.5155	0.1544	0.2495	-0.5899	0	0.3989	-0.0174	0.1466	0.6305	-0.1406	0.3737	-42.4233	198.954	37.4568
20	0.0487	-0.0729	-0.0038	0.0577	-0.028	0.0238	-0.1369	-0.2393	-0.4225	0.2557	0.113	-0.1001	0.4791	0.0365	-0	0.5486	-0.1626	0.2114	0.7582	-0.0042	0.564	-43.7104	189.8797	37.3806
21	0.0158	0.0079	0.0092	-0.001	0.0222	0.0223	0.0441	-0.0064	0.218	-0.134	0.0589	0.0447	-0.1995	-0.237	-0	0.4834	0.0494	-0.07	0.6755	-0.1304	0.6676	-44.7495	152.0543	-32.3856
22	0.0262	0.0208	-0.0211	0.0277	-0.0242	0.0185	-0.1241	0.2047	0.219	0.0304	0.0293	0.2163	-0.1698	-0.1018	0	0.4886	0.0354	-0.0442	0.427	-0.0178	0.4526	-36.9536	156.3329	-31.9296
23	0.037	0.0523	-0.0473	0.0182	-0.112	0.1705	0.1521	0.19	0.0379	-0.2244	-0.1661	0.049	-0.1174	-0.2753	-0	0.3326	0.0977	-0.0645	0.3574	-0.0774	0.4166	-40.866	154.7352	-22.3574
24	0.0181	0.0415	-0.0476	0.025	-0.0529	0.0011	-0.1144	-0.0861	-0.0304	-0.0914	0.2099	0.1171	-0.1204	0.2557	-0	0.3269	0.0408	-0.0364	0.2965	-0.0317	0.3704	-31.8528	154.7585	-23.9072
25	0.0205	0.0175	-0.0101	-0.0025	-0.0152	0.0257	-0.1581	0.077	-0.0277	-0.1123	-0.0857	0.3438	-0.26	-0.4366	-0	0.3542	0.1189	-0.0058	0.4269	-0.0156	0.4644	-41.289	158.1782	-11.7048
26	0.0162	0.0245	0.0081	-0.0356	0.0329	0.0191	0.0731	-0.0084	-0.1821	0.0672	-0.0329	-0.0312	0.0479	-0.0585	0	0.3195	0.019	-0.0003	0.2285	-0.0247	0.3719	-28.106	146.3094	-15.3716
27	0.0237	0.1048	-0.0218	0.0005	0.0704	-0.0172	-0.0367	-0.1569	0.0525	-0.3002	0.0564	0.1812	-0.1636	0.1017	0	0.2487	0.0094	-0.043	0.2405	-0.0467	0.3917	-26.185	155.4884	-16.7162
28	0.056	0.1542	0.056	0.1424	-0.1098	0.1369	-0.0664	0.0186	-0.0661	0.0435	0.0345	0.001	0.002	-0.0542	0	0.2624	0.0359	0.0265	0.2313	-0.0365	0.3414	-23.6446	154.7559	-7.8054
29	-0.0136	0.0959	0.0443	0.1702	0.1802	0.1526	-0.0463	-0.0247	0.0052	0.0851	0.005	-0.0012	0.1467	0.1055	0	0.2996	0.0385	0.0247	0.2101	-0.0203	0.2866	-17.8126	156.4107	0.5379
30	0.0238	0.0915	0.0177	0.0323	0.0143	-0.0217	0.0073	-0.007	-0.2112	0.0576	-0.0079	0.0635	-0.267	0.0443	-0	0.287	0.0158	0.0221	0.1997	-0.0381	0.2967	-15.785	164.1434	-4.3947
31	-0.0084	0.0861	-0.0308	0.2281	0.3369	0.1845	-0.014	0.0436	-0.0247	0.2245	0.0081	-0.0226	0.0896	0.078	0	0.3058	0.0275	0.0244	0.2344	-0.0248	0.2896	-12.827	167.0878	4.2987
32	-0.01	0.0138	-0.0424	0.0222	-0.0508	0.0213	0.1298	0.0945	-0.0011	-0.2744	-0.0856	0.0368	0.0675	-0.4579	0	0.4455	0.0817	0.0308	0.5027	-0.0638	0.4307	-26.3018	178.846	2.7566

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 12 through 66 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 67 through 82 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 83 through 166 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 167 through 208 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 209 through 234 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 235 through 250 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 251 through 274 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 275 through 293 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 23 through 40 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 41 through 124 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 125 through 166 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 167 through 276 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 277 through 291 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 15 through 39 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 40 through 66 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 67 through 82 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 83 through 166 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 167 through 250 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 251 through 276 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 277 through 292 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 12 through 24 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 25 through 41 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 42 through 66 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 67 through 82 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 83 through 94 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 95 through 108 )
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 109 through 124 )
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 125 through 166 )
29	X-RAY DIFFRACTION	29	chain 'D' and (resid 167 through 192 )
30	X-RAY DIFFRACTION	30	chain 'D' and (resid 193 through 208 )
31	X-RAY DIFFRACTION	31	chain 'D' and (resid 209 through 252 )
32	X-RAY DIFFRACTION	32	chain 'E' and (resid 1 through 10 )

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