PDB-5le7: Crystal structure of DARPin-DARPin rigid fusion, variant DD_D12_13_D12

ID or keywords:

Entry

Database: PDB / ID: 5le7

Title

Crystal structure of DARPin-DARPin rigid fusion, variant DD_D12_13_D12

Components

DD_D12_13_D12

Keywords

DE NOVO PROTEIN / designed ankyrin repeat proteins /

protein design /

protein engineering / rigid domain fusions

Biological species

synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.104 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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PDBx/mmCIF format	5le7.cif.gz	675.6 KB	Display	PDBx/mmCIF format
PDB format	pdb5le7.ent.gz	580.2 KB	Display	PDB format
PDBx/mmJSON format	5le7.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/le/5le7 ftp://data.pdbj.org/pub/pdb/validation_reports/le/5le7	HTTPS FTP

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Related structure data

Related structure data	5le2C 5le3C 5le4C 5le6C 5le8C 5le9C 5leaC 5lebC 5lecC 5ledC 5leeC 5lelC 5lemC 5lw2C 1svxS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	2x8x-d 3qdn-1 3dyj-1 3sz7-2 5h7b-2 5k35-d 1q4o-d 2d1a-d 4rvi-d 4kzd-3 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)

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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_13_D12

B: DD_D12_13_D12

C: DD_D12_13_D12

D: DD_D12_13_D12

hetero molecules

141 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: DD_D12_13_D12

hetero molecules

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

2

B: DD_D12_13_D12

hetero molecules

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

3

C: DD_D12_13_D12

hetero molecules

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

4

D: DD_D12_13_D12

hetero molecules

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

Unit cell

Length a, b, c (Å)	147.940, 75.250, 131.830
Angle α, β, γ (deg.)	90.00, 96.94, 90.00
Int Tables number	5
Space group name H-M	C121

#1: Protein	DD_D12_13_D12 Mass: 35193.320 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) / Variant (production host): XL1-Blue
#2: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 152 / 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: 2.59 Å³/Da / Density % sol: 52.46 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: PEG 3350 25% w/v, (NH4)2SO4 0.2 M, Bis-Tris 0.1 M, pH 5.5

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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: Oct 28, 2012
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.104→46.161 Å / Num. obs: 83045 / % possible obs: 99.19 % / Redundancy: 3.7 % / CC_1/2: 0.998 / R_merge(I) obs: 0.1079 / Net I/σ(I): 7.36
Reflection shell	Resolution: 2.104→46.161 Å / R_merge(I) obs: 2.694

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Processing

Software

Name	Version	Classification
XDS		data reduction
XSCALE		data scaling
PHASER		phasing
PHENIX	(dev_2386)	refinement

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1SVX chain A

1svx

Resolution: 2.104→46.161 Å / SU ML: 0.51 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 37.73

	R_factor	Num. reflection	% reflection
R_free	0.2579	4145	5 %
R_work	0.2254	-	-
obs	0.2271	82963	99.19 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.104→46.161 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9540	0	25	152	9717

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	9726
X-RAY DIFFRACTION	f_angle_d	0.489	13233
X-RAY DIFFRACTION	f_dihedral_angle_d	9.735	5735
X-RAY DIFFRACTION	f_chiral_restr	0.034	1531
X-RAY DIFFRACTION	f_plane_restr	0.003	1757

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 (%)
2.104-2.1279	0.5239	120	0.4871	2259	X-RAY DIFFRACTION	85
2.1279-2.153	0.4943	135	0.4797	2581	X-RAY DIFFRACTION	98
2.153-2.1792	0.4636	139	0.4471	2631	X-RAY DIFFRACTION	100
2.1792-2.2068	0.4376	138	0.4335	2620	X-RAY DIFFRACTION	100
2.2068-2.2358	0.3978	137	0.4022	2634	X-RAY DIFFRACTION	100
2.2358-2.2665	0.4061	137	0.4041	2614	X-RAY DIFFRACTION	100
2.2665-2.2989	0.4724	139	0.3943	2645	X-RAY DIFFRACTION	100
2.2989-2.3332	0.3842	136	0.389	2589	X-RAY DIFFRACTION	100
2.3332-2.3696	0.3894	141	0.3632	2681	X-RAY DIFFRACTION	100
2.3696-2.4085	0.3825	137	0.3567	2593	X-RAY DIFFRACTION	100
2.4085-2.45	0.3534	138	0.3492	2627	X-RAY DIFFRACTION	100
2.45-2.4945	0.3432	138	0.3441	2643	X-RAY DIFFRACTION	100
2.4945-2.5425	0.3274	137	0.3361	2628	X-RAY DIFFRACTION	100
2.5425-2.5944	0.3475	141	0.326	2664	X-RAY DIFFRACTION	100
2.5944-2.6508	0.3931	136	0.3256	2590	X-RAY DIFFRACTION	100
2.6508-2.7125	0.4144	138	0.3298	2636	X-RAY DIFFRACTION	100
2.7125-2.7803	0.3739	139	0.3013	2640	X-RAY DIFFRACTION	100
2.7803-2.8555	0.3127	139	0.2827	2645	X-RAY DIFFRACTION	100
2.8555-2.9395	0.2976	138	0.2542	2626	X-RAY DIFFRACTION	100
2.9395-3.0343	0.2932	139	0.2551	2624	X-RAY DIFFRACTION	100
3.0343-3.1428	0.273	139	0.2408	2652	X-RAY DIFFRACTION	99
3.1428-3.2686	0.2851	139	0.2415	2630	X-RAY DIFFRACTION	100
3.2686-3.4173	0.2844	139	0.2301	2640	X-RAY DIFFRACTION	100
3.4173-3.5974	0.2343	140	0.2096	2664	X-RAY DIFFRACTION	100
3.5974-3.8227	0.2072	138	0.1828	2627	X-RAY DIFFRACTION	100
3.8227-4.1176	0.2086	141	0.1711	2675	X-RAY DIFFRACTION	100
4.1176-4.5317	0.1945	139	0.155	2649	X-RAY DIFFRACTION	100
4.5317-5.1867	0.2126	141	0.1617	2679	X-RAY DIFFRACTION	100
5.1867-6.5317	0.2067	141	0.2042	2676	X-RAY DIFFRACTION	99
6.5317-46.1723	0.188	146	0.1641	2756	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	3.7791	1.0455	2.6703	1.0235	1.0597	1.9741	-0.0139	0.375	0.3482	0.0279	0.0449	0.1807	-0.1509	0.0531	-0.0871	1.0695	-0.064	0.2427	0.7899	-0.0001	0.6652	151.6891	-67.7254	18.0676
2	2.0659	-2.0228	-2.1145	4.1315	5.514	7.5777	-0.0112	0.2558	0.4157	0.0021	0.3353	-0.4858	0.0484	0.1902	-0.305	0.8421	-0.0858	0.0579	0.6623	-0.0361	0.6609	168.4817	-58.3562	35.238
3	1.7311	-2.0088	-0.7511	8.0381	3.1307	3.1958	-0.1102	-0.0111	-0.1917	0.1104	0.0387	-0.0634	0.289	-0.0286	0.083	0.4892	-0.0016	0.064	0.4231	0.0396	0.5082	164.9521	-35.2038	60.6025
4	4.7695	-1.7121	-0.2114	1.486	0.1543	1.0957	-0.0658	-0.0616	-0.0959	-0.0018	0.082	0.0164	0.1242	-0.0322	-0.0198	0.3945	-0.0344	0.0614	0.3083	0.023	0.3434	153.9692	0.1838	48.4196
5	1.6662	0.2174	0.5567	3.043	2.5277	5.6653	0.0413	0.0214	0.0402	-0.4155	-0.0367	0.1419	-0.1282	-0.1542	-0.0027	0.6657	-0.0547	0.0087	0.5578	0.013	0.4315	174.871	-20.131	10.957
6	4.5654	-1.8593	1.7347	2.1323	-0.4504	1.7303	0.1024	-0.1031	0.0176	-0.131	-0.0275	0.0137	-0.0704	-0.0575	-0.0802	0.4946	-0.0555	0.0279	0.3506	-0.0116	0.352	130.9169	-19.6716	45.5452
7	1.8828	0.1693	-0.6366	2.3398	-1.7424	4.1899	0.1586	0.2348	0.0296	-0.4942	-0.1167	-0.1801	0.5821	0.4762	-0.0213	1.0111	0.0581	0.0965	0.5939	-0.0358	0.4682	119.421	0.9649	4.3069
8	5.766	1.4492	-1.4707	1.4496	-0.6431	0.5794	0.0631	0.4015	-0.0087	0.0276	0.0955	-0.0953	-0.2452	0.1607	-0.1965	0.8822	-0.1006	-0.0317	0.7077	-0.0176	0.4363	140.5914	-26.2584	16.5072
9	2.308	0.9195	-1.3058	2.3664	-3.2633	4.4444	-0.0004	0.1933	-0.3725	-0.0584	-0.0282	-0.0546	-0.2795	-0.0091	0.0572	0.7387	-0.0328	-0.0125	0.489	-0.0193	0.4957	120.6224	-36.0887	28.9232
10	1.338	-1.1699	0.631	7.0935	-3.6571	4.2141	-0.0972	-0.0393	0.0707	0.2802	-0.0155	0.0649	-0.2183	0.0304	0.1039	0.3406	-0.0074	-0.0089	0.4398	-0.0207	0.4654	117.2725	-59.3234	54.2865

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 13 through 135 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 136 through 183 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 184 through 328 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 12 through 183 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 184 through 328 )
6	X-RAY DIFFRACTION	6	chain 'C' and (resid 11 through 183 )
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 184 through 328 )
8	X-RAY DIFFRACTION	8	chain 'D' and (resid 13 through 134 )
9	X-RAY DIFFRACTION	9	chain 'D' and (resid 135 through 183 )
10	X-RAY DIFFRACTION	10	chain 'D' and (resid 184 through 328 )

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