PDB-5le6: Crystal structure of DARPin-DARPin rigid fusion, variant DD_D12_09_D12

ID or keywords:

Entry

Database: PDB / ID: 5le6

Title

Crystal structure of DARPin-DARPin rigid fusion, variant DD_D12_09_D12

Components

DD_D12_09_D12

Keywords

DE NOVO PROTEIN / designed ankyrin repeat proteins / protein design / protein engineering / rigid domain fusions

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 /

MOLECULAR REPLACEMENT / Resolution: 1.8 Å

Authors

Batyuk, A. / Wu, Y. / Mittl, P.R. / Plueckthun, A.

Funding support

Switzerland, 2items

Citation

Journal: Sci Rep / Year: 2017
Title: Rigidly connected multispecific artificial binders with adjustable geometries.
Authors: Wu, Y. / Batyuk, A. / Honegger, A. / Brandl, F. / Mittl, P.R.E. / Pluckthun, A.

History

Deposition	Jun 29, 2016	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Aug 2, 2017	Provider: repository / Type: Initial release
Revision 1.1	Mar 20, 2019	Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2	Jan 10, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5le6.cif.gz	973.2 KB	Display	PDBx/mmCIF format
PDB format	pdb5le6.ent.gz	828.5 KB	Display	PDB format
PDBx/mmJSON format	5le6.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/le/5le6 ftp://data.pdbj.org/pub/pdb/validation_reports/le/5le6	HTTPS FTP

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Related structure data

Related structure data	5le2C 5le3C 5le4C 5le7C 5le8C 5le9C 5leaC 5lebC 5lecC 5ledC 5leeC 5lelC 5lemC 5lw2C 1svxS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5jk9-1 5jk9-5 5jk9-2 3qky-d 5jk9-6 3lne-d 2axw-d 5b5k-d 4uj8-4 4fvj-2 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) 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

Related structure data

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

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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: DD_D12_09_D12

B: DD_D12_09_D12

C: DD_D12_09_D12

D: DD_D12_09_D12

E: DD_D12_09_D12

F: DD_D12_09_D12

hetero molecules

210 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: DD_D12_09_D12

hetero molecules

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

2

B: DD_D12_09_D12

hetero molecules

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

3

C: DD_D12_09_D12

hetero molecules

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

4

D: DD_D12_09_D12

hetero molecules

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

5

E: DD_D12_09_D12

hetero molecules

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

6

F: DD_D12_09_D12

hetero molecules

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

Unit cell

Length a, b, c (Å)	145.120, 145.120, 376.760
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	178
Space group name H-M	P6₁22

#1: Protein	DD_D12_09_D12 Mass: 34852.227 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli K-12 (bacteria) / Variant (production host): XL1-Blue
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1758 / 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: 2.74 Å³/Da / Density % sol: 55.08 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: PEG 3350 17% w/v, Na2SO4 0.2 M

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 16, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.8→48.26 Å / Num. obs: 215348 / % possible obs: 99.94 % / Redundancy: 38.9 % / CC_1/2: 0.999 / R_merge(I) obs: 0.217 / Net I/σ(I): 19.99
Reflection shell	Resolution: 1.8→1.864 Å / R_merge(I) obs: 4.336

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Processing

Software

Name	Version	Classification
XDS		data reduction
XSCALE		data scaling
PHASER		phasing
PHENIX	(dev_2429)	refinement

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1SVX chain A

1svx

Resolution: 1.8→48.26 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.7

	R_factor	Num. reflection	% reflection
R_free	0.2264	10764	5 %
R_work	0.1922	-	-
obs	0.1939	215232	99.94 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.8→48.26 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13320	0	75	1758	15153

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	13677
X-RAY DIFFRACTION	f_angle_d	0.727	18632
X-RAY DIFFRACTION	f_dihedral_angle_d	10.413	7974
X-RAY DIFFRACTION	f_chiral_restr	0.043	2190
X-RAY DIFFRACTION	f_plane_restr	0.005	2421

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 (%)
1.8-1.8205	0.3861	354	0.3558	6730	X-RAY DIFFRACTION	100
1.8205-1.8419	0.3491	355	0.3455	6726	X-RAY DIFFRACTION	100
1.8419-1.8644	0.3632	354	0.3246	6717	X-RAY DIFFRACTION	100
1.8644-1.888	0.3386	354	0.3067	6744	X-RAY DIFFRACTION	100
1.888-1.9128	0.3335	353	0.3099	6687	X-RAY DIFFRACTION	100
1.9128-1.939	0.3478	354	0.3026	6739	X-RAY DIFFRACTION	100
1.939-1.9667	0.3147	354	0.2751	6730	X-RAY DIFFRACTION	100
1.9667-1.9961	0.2946	353	0.2581	6715	X-RAY DIFFRACTION	100
1.9961-2.0272	0.2895	356	0.248	6745	X-RAY DIFFRACTION	100
2.0272-2.0605	0.2839	354	0.232	6730	X-RAY DIFFRACTION	100
2.0605-2.096	0.2734	354	0.2265	6730	X-RAY DIFFRACTION	100
2.096-2.1341	0.2582	358	0.2216	6797	X-RAY DIFFRACTION	100
2.1341-2.1752	0.2334	353	0.2033	6700	X-RAY DIFFRACTION	100
2.1752-2.2196	0.2253	357	0.195	6773	X-RAY DIFFRACTION	100
2.2196-2.2678	0.2289	357	0.1943	6795	X-RAY DIFFRACTION	100
2.2678-2.3206	0.2302	355	0.1926	6744	X-RAY DIFFRACTION	100
2.3206-2.3786	0.2368	358	0.187	6801	X-RAY DIFFRACTION	100
2.3786-2.4429	0.2415	356	0.1835	6764	X-RAY DIFFRACTION	100
2.4429-2.5148	0.22	359	0.184	6804	X-RAY DIFFRACTION	100
2.5148-2.596	0.225	357	0.1754	6795	X-RAY DIFFRACTION	100
2.596-2.6888	0.2279	360	0.1742	6825	X-RAY DIFFRACTION	100
2.6888-2.7964	0.2137	359	0.1769	6823	X-RAY DIFFRACTION	100
2.7964-2.9237	0.2253	359	0.1844	6821	X-RAY DIFFRACTION	100
2.9237-3.0778	0.2371	361	0.1926	6856	X-RAY DIFFRACTION	100
3.0778-3.2706	0.2138	361	0.1916	6854	X-RAY DIFFRACTION	100
3.2706-3.523	0.2124	363	0.1794	6906	X-RAY DIFFRACTION	100
3.523-3.8774	0.1974	365	0.1654	6931	X-RAY DIFFRACTION	100
3.8774-4.4381	0.187	367	0.1574	6983	X-RAY DIFFRACTION	100
4.4381-5.5903	0.1824	372	0.161	7076	X-RAY DIFFRACTION	100
5.5903-48.2771	0.2122	392	0.1911	7427	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	0.7669	0.4089	-0.1415	0.8887	-0.0465	0.8739	-0.1569	0.1028	-0.003	-0.1914	0.0199	-0.1824	0.1073	0.0397	-0	0.2543	-0.0106	0.0397	0.2847	0.0602	0.2171	50.5551	68.2222	-15.5696
2	0.1432	0.3989	-0.049	1.1149	-0.4288	0.1283	-0.0504	0.13	-0.0169	-0.1267	0.0613	-0.1587	-0.0386	-0.0992	-0	0.3315	-0.0016	0.0421	0.2759	0.0328	0.2725	44.6467	44.2355	-5.163
3	0.7487	-0.2981	-0.3055	0.7525	0.231	0.8912	0.0007	0.0392	-0.2003	0.0158	-0.0769	0.1574	0.0181	-0.1457	0	0.2528	0.0098	0.0192	0.2655	-0.0012	0.2506	26.9202	24.1063	6.223
4	1.2367	-0.3277	0.5991	0.3249	0.3268	0.6599	-0.0697	0.1725	0.1876	-0.0447	-0.0602	-0.1098	-0.0275	0.0284	-0.0001	0.2846	-0.0124	0.0099	0.2708	0.0564	0.2105	59.5773	15.2982	-12.711
5	0.756	-0.0307	0.0029	0.7513	-0.5815	0.9315	-0.0423	-0.0068	-0.0244	-0.0794	-0.0117	-0.2728	0.1259	0.0034	0	0.2694	0.0042	-0.0008	0.221	0.0264	0.4008	101.0837	15.5526	4.4569
6	0.6553	0.0502	0.6238	0.7077	-0.0215	0.8868	-0.0186	-0.0446	0.2413	0.2202	-0.1333	0.125	0.0276	-0.0555	-0	0.3233	-0.0063	0.0266	0.2763	-0.0455	0.3216	27.6469	81.5754	15.2558
7	0.8361	0.9486	0.3138	0.7955	0.1429	0.332	0.0705	-0.0655	0.1784	0.0016	-0.0819	0.1759	0.008	-0.0462	-0	0.2669	-0.0199	0.0317	0.2839	-0.036	0.3444	9.8093	64.4227	5.1053
8	0.8181	-0.1044	-0.368	0.4358	0.344	0.5031	-0.0582	-0.0654	-0.1304	0.0054	0.0131	0.0681	0.1207	0.0099	0	0.2526	0.0099	0.0324	0.241	0.0189	0.276	1.3236	41.9932	-5.1535
9	0.0402	-0.0646	0.0151	0.092	0.0227	0.1704	0.0511	-0.015	-0.248	-0.1627	-0.1637	0.2045	0.6806	0.0219	-0.0007	0.4858	-0.0446	0.1196	0.2683	-0.0184	0.5583	0.0707	24.7787	-11.0464
10	0.9163	-0.2029	-0.2346	0.7881	-0.3934	0.9274	-0.0734	-0.1432	-0.2394	-0.0286	-0.005	-0.1615	0.185	0.0238	-0.0001	0.3444	0.0441	-0.0328	0.2945	0.093	0.3966	102.589	-5.0487	20.0888
11	1.3795	-0.1431	0.589	0.0735	-0.1324	0.4048	0.0275	-0.0776	0.0367	-0.0046	-0.0549	-0.0178	0.0841	-0.0074	0	0.2791	0.0174	-0.0022	0.2416	-0.0018	0.2164	61.7364	11.5134	12.0286
12	1.1334	-0.3514	-0.3342	0.7209	-0.1983	0.7943	-0.1888	-0.0995	-0.3628	-0.1977	0.0477	-0.0142	0.2474	0.1254	-0.0014	0.4075	0.0463	0.1091	0.2777	0.0216	0.3132	18.8934	28.2733	-19.6149
13	0.0023	0.0263	-0.017	0.837	-0.5405	0.3555	-0.2512	-0.1894	-0.0148	-0.335	-0.119	-0.3946	-0.121	0.1249	-0.0582	0.3593	0.0121	0.0483	0.3073	-0.0337	0.2342	21.2032	46.947	-23.5783
14	0.5021	0.4913	0.1377	1.1048	0.3441	0.1512	-0.0783	0.0753	0.1625	-0.0117	0.0318	0.0622	0.0148	0.0508	-0	0.2756	0.0092	-0.0174	0.252	0.0541	0.301	25.3672	74.3646	-12.0693
15	0.6226	0.2053	0.1883	0.8098	0.1713	0.2715	0.0192	-0.0489	-0.0845	0.1604	-0.0872	0.3748	-0.0017	-0.1741	-0	0.2928	0.0183	0.0841	0.396	0.0022	0.3263	8.7211	34.3092	19.503
16	0.9515	0.9725	-0.4856	1.3709	-0.5486	0.2271	-0.0282	0.0066	0.0389	0.1357	-0.0249	-0.12	-0.022	0.0327	0	0.2712	-0.0012	-0.0381	0.2606	0.0393	0.1996	43.5652	61.5603	12.7951

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 14 through 125 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 126 through 204 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 205 through 324 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 14 through 179 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 180 through 324 )
6	X-RAY DIFFRACTION	6	chain 'C' and (resid 14 through 125 )
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 126 through 204 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 205 through 303 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 304 through 324 )
10	X-RAY DIFFRACTION	10	chain 'D' and (resid 14 through 158 )
11	X-RAY DIFFRACTION	11	chain 'D' and (resid 159 through 324 )
12	X-RAY DIFFRACTION	12	chain 'E' and (resid 14 through 125 )
13	X-RAY DIFFRACTION	13	chain 'E' and (resid 126 through 158 )
14	X-RAY DIFFRACTION	14	chain 'E' and (resid 159 through 324 )
15	X-RAY DIFFRACTION	15	chain 'F' and (resid 14 through 125 )
16	X-RAY DIFFRACTION	16	chain 'F' and (resid 126 through 324 )

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