PDB-5kwd: Computationally Designed Symmetric Homotetramer

ID or keywords:

Entry

Database: PDB / ID: 5kwd

Title

Computationally Designed Symmetric Homotetramer

Components

Ankyrin repeat-containing protein

Keywords

DE NOVO PROTEIN / homooligomer / designed protein / ankyrin / repeat protein

Function / homology

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

Function and homology information

Biological species

Metallosphaera yellowstonensis MK1 (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.75 Å

Authors

Fallas, J.A. / Sankaran, B. / Zwart, P. / Baker, D.

Funding support

United States, 1items

Citation

Journal: Nat Chem / Year: 2017
Title: Computational design of self-assembling cyclic protein homo-oligomers.
Authors: Fallas, J.A. / Ueda, G. / Sheffler, W. / Nguyen, V. / McNamara, D.E. / Sankaran, B. / Pereira, J.H. / Parmeggiani, F. / Brunette, T.J. / Cascio, D. / Yeates, T.R. / Zwart, P. / Baker, D.

History

Deposition	Jul 17, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 12, 2017	Provider: repository / Type: Initial release
Revision 1.1	Sep 20, 2017	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2	Nov 27, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3	Mar 6, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5kwd.cif.gz	337 KB	Display	PDBx/mmCIF format
PDB format	pdb5kwd.ent.gz	283.9 KB	Display	PDB format
PDBx/mmJSON format	5kwd.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5kwd_validation.pdf.gz	454.6 KB	Display	wwPDB validaton report
Full document	5kwd_full_validation.pdf.gz	469 KB	Display
Data in XML	5kwd_validation.xml.gz	22.2 KB	Display
Data in CIF	5kwd_validation.cif.gz	30.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/kw/5kwd ftp://data.pdbj.org/pub/pdb/validation_reports/kw/5kwd	HTTPS FTP

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Related structure data

Related structure data	4gmrC 4gpmC 4hb5C 4hxtC 5hryC 5hrzC 5hs0C 5k7vC 5kbaC C: citing same article (ref.)
Similar structure data	4w8p-2 2xig-d 3nob-d 6twn-d 1u04-d 6onw-d 3m4g-d 4my3-2 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 (2) #259 - Jul 2021 Designed Proteins and Citizen Science similarity (1)

Deposited unit

A: Ankyrin repeat-containing protein

B: Ankyrin repeat-containing protein

C: Ankyrin repeat-containing protein

D: Ankyrin repeat-containing protein

69.5 kDa, 4 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)	77.770, 89.470, 99.080
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Ankyrin repeat-containing protein Mass: 17364.436 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Metallosphaera yellowstonensis MK1 (archaea) Gene: MetMK1DRAFT_00016260 / Production host: Escherichia coli BL21 (bacteria)
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 36 / 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: 2.5 Å³/Da / Density % sol: 50.73 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 2.1M DL-Malic acid pH 7.0

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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: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 28, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.38→66.403 Å / Num. obs: 27140 / % possible obs: 97.13 % / Redundancy: 2 % / Net I/σ(I): 3
Reflection shell	Resolution: 2.75→2.82 Å / Redundancy: 1.9 % / R_merge(I) obs: 0.64 / Mean I/σ(I) obs: 1.1 / CC_1/2: 0.53 / % possible all: 100

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.75→66.403 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29

	R_factor	Num. reflection	% reflection
R_free	0.2811	1851	10.01 %
R_work	0.2292	-	-
obs	0.2345	18494	99.68 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.75→66.403 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4718	0	0	36	4754

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	4802
X-RAY DIFFRACTION	f_angle_d	0.521	6525
X-RAY DIFFRACTION	f_dihedral_angle_d	10.824	2911
X-RAY DIFFRACTION	f_chiral_restr	0.037	750
X-RAY DIFFRACTION	f_plane_restr	0.004	878

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 (%)
2.75-2.8244	0.3347	139	0.2936	1248	X-RAY DIFFRACTION	100
2.8244-2.9075	0.3804	141	0.2707	1271	X-RAY DIFFRACTION	100
2.9075-3.0013	0.2803	140	0.2536	1263	X-RAY DIFFRACTION	100
3.0013-3.1086	0.3039	140	0.2351	1263	X-RAY DIFFRACTION	100
3.1086-3.233	0.2939	140	0.2377	1258	X-RAY DIFFRACTION	100
3.233-3.3802	0.3081	141	0.2478	1265	X-RAY DIFFRACTION	100
3.3802-3.5584	0.2836	140	0.2353	1257	X-RAY DIFFRACTION	100
3.5584-3.7813	0.2854	141	0.2531	1262	X-RAY DIFFRACTION	99
3.7813-4.0732	0.2831	142	0.2305	1285	X-RAY DIFFRACTION	99
4.0732-4.483	0.251	142	0.2031	1273	X-RAY DIFFRACTION	100
4.483-5.1315	0.2617	145	0.1941	1304	X-RAY DIFFRACTION	100
5.1315-6.4643	0.332	146	0.2481	1311	X-RAY DIFFRACTION	100
6.4643-66.4224	0.2216	154	0.1916	1383	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	6.5439	3.3612	0.9718	5.8068	0.5501	6.199	0.3094	0.1752	-0.052	0.6672	-0.1224	0.0023	0.2859	-0.1705	-0.218	0.5776	0.0209	0.0743	0.3765	0.0303	0.3288	6.8745	15.38	-14.1655
2	5.1493	2.0076	-2.0698	5.3437	1.2276	2.1545	0.366	0.2618	0.0977	0.1132	-0.1759	-0.0496	0.0151	-0.3526	-0.2407	0.362	0.0424	-0.0329	0.379	0.0288	0.2598	1.9685	12.8695	-4.4481
3	3.7998	0.0715	-0.4669	3.6989	-0.6511	7.0046	0.1044	-0.4884	0.1492	0.3164	-0.1304	-0.1132	-0.0619	0.1839	0.0055	0.3028	-0.0154	-0.0084	0.3092	-0.0007	0.2741	3.6334	12.7526	15.2601
4	4.2293	5.9111	-1.9186	9.0136	-4.7161	6.298	0.2364	0.9854	0.202	0.6892	0.3147	-0.077	-0.3727	-0.3589	-0.3841	0.7102	0.0233	-0.0926	0.4106	-0.0355	0.41	-6.8331	-8.3528	-20.5683
5	2.5941	1.1906	2.0487	3.4179	2.4	4.5418	0.2454	-0.0079	-0.2727	0.6249	-0.0406	-0.2017	0.2147	-0.0013	-0.163	0.8161	-0.0978	-0.0295	0.3954	0.0093	0.5048	-4.3804	-11.9906	-18.621
6	5.493	1.161	1.4286	4.3316	0.8315	5.5723	-0.1236	-0.14	-0.2413	0.0505	-0.0086	-0.071	-0.1408	-0.3121	0.1783	0.4698	-0.0797	0.0787	0.3805	0.0032	0.3459	-5.9296	-13.3167	-8.9953
7	2.7415	1.1735	-0.4137	2.1834	0.7912	4.509	-0.1165	-0.2857	0.2276	0.3855	-0.2698	0.4608	0.411	-0.1117	0.3794	0.4512	-0.1098	0.0405	0.412	0.002	0.4555	-9.0982	-12.8692	4.7663
8	2.375	0.2132	2.0179	8.0025	-2.0564	2.4586	-0.7512	-0.4053	0.257	0.1168	0.0114	-0.8066	-0.203	-0.2255	0.723	0.6372	-0.0271	-0.0234	0.5414	-0.048	0.5848	-14.9912	-13.7205	16.3026
9	9.8237	-3.093	2.5938	9.8326	-2.1451	2.097	0.4765	-0.3762	-0.8723	-0.8863	-0.3604	-0.2947	0.9931	0.3053	-0.1193	0.5679	0.0371	0.0077	0.4165	0.0393	0.4347	-28.9072	5.7409	19.1643
10	3.8438	-1.7214	0.178	4.4366	0.1764	2.5337	0.2129	0.6523	-0.0804	-0.5943	-0.0834	-0.1248	0.8558	0.0702	-0.0701	0.6864	-0.0128	-0.0456	0.4214	0.0272	0.2924	-26.0878	7.74	15.6945
11	2.8654	-0.9914	0.1855	6.7399	-0.8358	3.517	0.0958	0.106	-0.4181	-0.1402	-0.1557	-0.4561	0.4137	0.5475	0.0281	0.41	0.0282	0.0009	0.4768	-0.0428	0.4398	-28.0193	4.2762	6.8343
12	6.6591	-1.7716	-0.0395	5.7466	0.8098	7.1692	0.0943	-0.1352	-0.215	0.1824	0.0177	0.0109	1.0865	0.7985	-0.1038	0.4958	0.0522	-0.0948	0.4684	0.0151	0.3502	-31.9451	-1.0325	-2.3289
13	1.6227	-0.661	0.5421	2.0774	-1.8409	3.5696	0.4458	0.099	-0.5231	-0.2866	-0.2662	-0.1617	0.8935	0.6455	-0.0862	0.5577	0.1097	-0.0926	0.5795	-0.0317	0.6155	-32.2551	-5.3771	-10.1048
14	5.4002	-0.8872	-2.5381	3.8069	-0.1776	7.6283	-0.0527	0.2025	-0.1953	0.283	-0.4315	0.1475	0.9081	-0.8444	0.4356	0.6226	-0.1236	-0.0618	0.5185	-0.0945	0.4444	-39.148	-6.3473	-15.259
15	6.8597	-1.8684	0.8015	8.3696	5.1997	4.9397	-0.2398	-0.8519	-0.4997	0.0995	0.4423	-0.1761	-0.7256	0.1792	-0.2697	0.5222	0.0271	-0.1086	0.4118	0.0948	0.4093	25.8281	-8.5822	28.1354
16	2.3714	-2.7133	-2.3392	7.2929	-1.7717	7.9191	0.0371	-0.3458	0.0495	0.3022	0.3362	-0.6135	1.3646	-0.3734	-0.3458	0.7813	0.0466	-0.1579	0.3884	-0.0011	0.3762	27.2406	-17.6879	25.572
17	4.0636	1.8571	0.887	3.4482	-2.2459	3.5506	-0.2018	-0.585	0.031	-1.9389	0.1355	0.9588	0.4641	0.0466	0.0729	0.5454	0.0584	-0.035	0.5508	0.046	0.4615	18.9054	-6.5512	24.9614
18	5.1989	-2.5625	0.6253	2.6529	1.1937	3.5027	0.0988	0.1583	0.2827	-0.0213	0.0617	-0.2804	-0.126	-0.2997	-0.1673	0.4286	0.1022	0.0408	0.2715	0.0385	0.3307	21.7539	-8.1583	16.3868
19	7.2141	0.4872	0.3561	4.5199	-0.0789	3.5667	0.397	0.4064	-0.3745	-0.1287	-0.2156	-0.4671	0.4828	0.0514	-0.1927	0.455	0.0922	-0.0313	0.4424	-0.0177	0.3724	23.7663	-7.8072	8.1009
20	0.9111	-0.9007	-0.7774	4.1154	-1.3748	2.1485	0.2203	-0.5258	-0.0493	-0.8504	-0.624	0.4048	-0.1247	0.1821	0.3839	0.469	0.1109	-0.0996	0.555	-0.0422	0.4432	16.1611	2.3089	7.0883
21	3.2636	-1.18	0.219	3.9765	0.877	3.1955	0.3324	-0.4699	-0.3109	-0.5095	-0.4018	-0.6205	0.2038	0.5237	0.0023	0.3836	0.1626	0.0671	0.5488	0.0744	0.4208	24.2103	-2.3588	0.4915
22	1.5021	0.3421	-1.0387	5.044	-2.6274	1.8624	-0.1483	0.4134	0.1686	-0.7339	0.0439	0.0923	-0.121	-0.3989	0.1379	0.4122	0.0067	0.0006	0.5878	0.1089	0.3704	16.7421	7.3987	-0.3627
23	3.6409	-0.0282	-2.5777	2.1011	2.5388	9.7656	-0.1944	0.4443	-0.0031	-0.5443	-0.0465	-0.2537	-0.2717	-0.0238	0.3544	0.5662	0.1194	-0.018	0.5866	0.0203	0.5416	24.1537	3.5434	-7.7872

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 24 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 25 through 71 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 72 through 160 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 1 through 13 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 14 through 38 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 39 through 71 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 72 through 137 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 138 through 160 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 1 through 13 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 14 through 38 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 39 through 71 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 72 through 114 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 115 through 137 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 138 through 158 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 1 through 13 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 14 through 24 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 25 through 38 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 39 through 71 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 72 through 91 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 92 through 104 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 105 through 124 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 125 through 137 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 138 through 159 )

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