PDB-6fpa: Crystal structure of anti-mTFP1 DARPin 1238_G01 in space group P212121

ID or keywords:

Entry

Database: PDB / ID: 6fpa

Title

Crystal structure of anti-mTFP1 DARPin 1238_G01 in space group P212121

Components

DARPin 1238_G01

Keywords

DE NOVO PROTEIN /

Darpin / protein binder / designed ankyrin repeat proteins

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: 1.58 Å

Authors

Jakob, R.P. / Vigano, M.A. / Bieli, D. / Matsuda, S. / Schaefer, J.V. / Pluckthun, A. / Affolter, M. / Maier, T.

Citation

Journal: Biol Open / Year: 2018
Title: DARPins recognizing mTFP1 as novel reagents forin vitroandin vivoprotein manipulations.
Authors: Vigano, M.A. / Bieli, D. / Schaefer, J.V. / Jakob, R.P. / Matsuda, S. / Maier, T. / Pluckthun, A. / Affolter, M.

History

Deposition	Feb 9, 2018	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Oct 3, 2018	Provider: repository / Type: Initial release
Revision 1.1	Nov 7, 2018	Group: Data collection / Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.title / _citation_author.identifier_ORCID
Revision 1.2	Dec 26, 2018	Group: Data collection / Database references / Category: citation / Item: _citation.title
Revision 1.3	Jan 17, 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	6fpa.cif.gz	197.5 KB	Display	PDBx/mmCIF format
PDB format	pdb6fpa.ent.gz	162.6 KB	Display	PDB format
PDBx/mmJSON format	6fpa.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/fp/6fpa ftp://data.pdbj.org/pub/pdb/validation_reports/fp/6fpa	HTTPS FTP

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Related structure data

Related structure data	6fp7C 6fp8C 6fp9C 6fpbC 4ydyS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5cgb-2 2bsc-d 6s09-1 4gmr-2 1aep-d 6g2s-4 4avk-2 5lp9-d 6s09-2 4hb5-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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: DARPin 1238_G01

B: DARPin 1238_G01

34.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: DARPin 1238_G01

defined by author
Evidence: gel filtration
17.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: DARPin 1238_G01

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

Unit cell

Length a, b, c (Å)	37.990, 89.156, 103.838
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	DARPin 1238_G01 Mass: 17364.582 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Plasmid: pQiq / Production host: Escherichia coli (E. coli) / Strain (production host): XL1Blue
#2: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 569 / 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: 2.53 Å³/Da / Density % sol: 51.42 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4 / Details: 0.2 M NaF, 20% PEG3350

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99986 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 19, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.99986 Å / Relative weight: 1
Reflection	Resolution: 1.58→44.578 Å / Num. obs: 92607 / % possible obs: 99.2 % / Redundancy: 4.6 % / CC_1/2: 0.999 / R_rim(I) all: 0.078 / Net I/σ(I): 14.1
Reflection shell	Resolution: 1.58→1.68 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 4720 / CC_1/2: 0.51 / R_rim(I) all: 1.19 / % possible all: 97

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Processing

Software

Name	Version	Classification
PHENIX	(1.10pre_2131: ???)	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4YDY

4ydy

Resolution: 1.58→44.578 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.18 / Phase error: 17.68

	R_factor	Num. reflection	% reflection
R_free	0.18	4646	5.02 %
R_work	0.1454	-	-
obs	0.1471	92607	99.14 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.58→44.578 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2409	0	0	573	2982

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	2490
X-RAY DIFFRACTION	f_angle_d	0.859	3388
X-RAY DIFFRACTION	f_dihedral_angle_d	12.996	1500
X-RAY DIFFRACTION	f_chiral_restr	0.05	394
X-RAY DIFFRACTION	f_plane_restr	0.006	452

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 (%)
1.5796-1.5976	0.3227	138	0.3053	2607	X-RAY DIFFRACTION	89
1.5976-1.6164	0.3523	150	0.2901	2913	X-RAY DIFFRACTION	99
1.6164-1.6361	0.2993	153	0.2816	2927	X-RAY DIFFRACTION	99
1.6361-1.6568	0.2694	156	0.2682	2919	X-RAY DIFFRACTION	99
1.6568-1.6786	0.2796	153	0.2526	2946	X-RAY DIFFRACTION	99
1.6786-1.7016	0.2959	155	0.2471	2942	X-RAY DIFFRACTION	99
1.7016-1.7259	0.2468	160	0.2299	2966	X-RAY DIFFRACTION	99
1.7259-1.7517	0.2423	155	0.2195	2891	X-RAY DIFFRACTION	99
1.7517-1.779	0.2315	154	0.2049	2955	X-RAY DIFFRACTION	99
1.779-1.8082	0.2197	160	0.2087	2978	X-RAY DIFFRACTION	99
1.8082-1.8394	0.2386	152	0.192	2912	X-RAY DIFFRACTION	100
1.8394-1.8728	0.2063	153	0.1884	2929	X-RAY DIFFRACTION	99
1.8728-1.9089	0.2398	155	0.166	2959	X-RAY DIFFRACTION	100
1.9089-1.9478	0.1896	152	0.1549	2932	X-RAY DIFFRACTION	100
1.9478-1.9902	0.1615	157	0.1491	2968	X-RAY DIFFRACTION	100
1.9902-2.0365	0.1511	156	0.1413	2951	X-RAY DIFFRACTION	100
2.0365-2.0874	0.1723	155	0.1344	2975	X-RAY DIFFRACTION	100
2.0874-2.1438	0.1509	153	0.1376	2960	X-RAY DIFFRACTION	100
2.1438-2.2069	0.1681	160	0.13	2931	X-RAY DIFFRACTION	100
2.2069-2.2781	0.1484	157	0.1294	2921	X-RAY DIFFRACTION	99
2.2781-2.3596	0.1444	159	0.1285	2972	X-RAY DIFFRACTION	100
2.3596-2.454	0.1714	159	0.1257	2912	X-RAY DIFFRACTION	99
2.454-2.5657	0.1657	159	0.1218	2947	X-RAY DIFFRACTION	100
2.5657-2.701	0.1776	155	0.1252	2938	X-RAY DIFFRACTION	99
2.701-2.8702	0.164	155	0.1336	2950	X-RAY DIFFRACTION	100
2.8702-3.0917	0.1658	156	0.1326	2964	X-RAY DIFFRACTION	100
3.0917-3.4027	0.1978	161	0.1336	2940	X-RAY DIFFRACTION	100
3.4027-3.8949	0.1614	157	0.1227	2963	X-RAY DIFFRACTION	100
3.8949-4.9061	0.138	149	0.1129	2956	X-RAY DIFFRACTION	99
4.9061-44.5957	0.1907	152	0.1536	2937	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	7.2397	-1.7182	-0.7645	6.6631	1.1682	5.4493	0.167	0.4283	0.7106	-0.5419	-0.1244	0.3272	-0.8643	-0.5132	0.0204	0.279	0.0653	-0.0131	0.1972	0.011	0.2469	9.3411	5.4014	-4.401
2	1.4824	-0.2618	0.8067	2.6898	1.022	2.0398	0.039	-0.0514	0.0795	-0.1316	0.027	0.0449	-0.0629	0.0297	-0.0625	0.1483	-0.0021	0.0082	0.1586	0.0003	0.1517	13.6009	-1.3872	-2.1206
3	0.8525	0.0667	-0.2712	1.8468	-0.3247	5.0773	0.0466	0.0095	-0.1012	-0.0814	0.0807	0.1813	0.1248	-0.0732	-0.201	0.1631	0.004	-0.0256	0.161	0.0069	0.1789	8.9544	-11.4628	-6.5183
4	4.137	0.4046	-0.4612	3.449	0.5331	3.0101	0.0728	-0.0806	0.0161	0.0925	0.0741	-0.2754	0.1192	0.2134	-0.0655	0.1746	0.0205	-0.0129	0.1528	-0.0313	0.1824	20.2803	-13.8096	-6.4251
5	1.5107	-0.1912	1.0597	1.0599	-0.3177	1.3848	0.2058	0.0885	-0.2064	-0.1372	-0.0112	0.2651	0.1524	0.039	-0.1517	0.2492	0.0112	-0.0539	0.1619	-0.0062	0.2254	11.2463	-19.8191	-12.2021
6	3.1115	-0.5857	-1.0578	4.5628	0.9305	2.184	0.0776	0.1843	-0.1105	-0.4436	-0.0662	0.0952	0.1351	0.1161	-0.0345	0.2441	0.0363	-0.0384	0.1374	-0.016	0.1581	20.2897	-23.1293	-16.8577
7	3.9976	2.4104	-1.0182	4.1565	-1.0142	1.448	0.1091	0.0988	-0.4511	-0.6083	-0.171	-0.3022	0.362	0.2842	0.2378	0.3008	0.0755	-0.0099	0.2304	-0.0175	0.2457	26.9199	-31.2021	-16.2515
8	4.4401	-0.7612	0.2259	6.0158	0.3072	5.9426	0.0045	0.5321	0.2804	-0.1265	-0.1407	-0.3873	-0.2126	1.2096	0.1768	0.1863	-0.0132	-0.0368	0.3822	0.0052	0.213	51.811	-2.838	-30.1495
9	2.6037	0.7464	0.0538	2.3067	0.1146	4.8355	0.1505	0.0774	-0.2353	0.17	-0.176	-0.1185	-0.092	0.5697	0.0118	0.2357	-0.0011	-0.0647	0.2432	0.0018	0.2048	51.4663	-7.4315	-21.9507
10	1.1492	0.1968	0.6733	1.8724	0.06	4.252	-0.0482	0.127	0.0542	0.1563	0.0518	0.0711	-0.2727	0.0604	0.0168	0.172	-0.0404	-0.0171	0.1878	0.0188	0.1846	45.6529	1.6926	-31.2587
11	2.7853	-1.0947	1.1125	3.6241	0.2266	1.4111	0.2021	-0.0093	-0.3082	0.1113	0.0268	-0.0506	0.3167	0.1322	-0.2322	0.1969	0.0122	-0.0601	0.1694	-0.0091	0.1781	41.303	-9.505	-28.1868
12	0.8412	-0.1124	-0.8347	1.0886	-0.207	4.9485	-0.0194	0.0738	0.0742	0.1108	0.0531	0.0219	0.0318	-0.0975	-0.0547	0.1568	-0.005	-0.0093	0.1608	0.0175	0.1695	35.7546	-0.5847	-34.3956
13	2.9131	-0.4796	0.8051	3.7179	0.4053	2.9659	0.2503	0.0687	-0.4743	0.13	-0.0021	0.0221	0.4114	0.1436	-0.2042	0.1878	0.0019	-0.0749	0.1675	-0.0019	0.2086	33.8066	-12.5874	-33.4714
14	1.7173	0.1943	0.4054	1.3998	-0.8483	0.7442	0.072	0.0881	0.0869	0.0279	0.043	0.1275	-0.0515	0.1323	-0.0536	0.1596	-0.0223	-0.011	0.1887	0.0206	0.1883	28.1721	-3.4016	-39.6674
15	1.5069	-1.1966	0.5667	4.3456	-0.157	1.7617	0.1502	0.4279	-0.1324	-0.1363	-0.1257	-0.1392	0.1524	0.3199	-0.0425	0.1469	0.0404	-0.0307	0.2442	-0.0277	0.2041	31.3525	-13.1046	-44.5275
16	5.349	-1.572	-0.5296	6.9681	2.5452	7.2166	0.0887	-0.2432	-0.8428	0.7046	0.0228	0.1584	0.8866	-0.116	-0.0797	0.241	-0.0372	-0.0391	0.1636	0.0155	0.2601	25.3696	-18.0461	-37.077
17	1.7578	0.133	-0.0102	3.3897	-2.5714	5.1305	0.054	0.3595	0.1668	0.0247	-0.0713	0.1825	-0.2289	0.3618	-0.0598	0.1286	-0.0309	-0.0349	0.2105	0.0263	0.2099	21.9215	-6.8117	-45.4857
18	2.4764	-0.365	-0.5028	2.9416	0.4822	2.4207	0.2203	0.7485	-0.3491	-0.3664	-0.0739	0.0406	0.2676	0.327	-0.1122	0.2155	0.0704	-0.0349	0.3095	-0.0828	0.2155	26.5604	-15.2217	-51.7716
19	6.3833	-0.9608	0.0591	5.6129	-0.0478	3.3691	0.2347	0.5447	-0.8405	-0.0173	-0.2594	0.969	0.3758	-0.4261	0.0773	0.2308	-0.0366	-0.0691	0.2664	-0.087	0.3794	18.0771	-19.2498	-46.1863

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 13 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 14 through 57 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 58 through 72 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 73 through 91 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 92 through 105 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 106 through 148 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 149 through 162 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 3 through 14 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 15 through 25 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 26 through 39 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 40 through 58 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 59 through 72 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 73 through 91 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 92 through 105 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 106 through 115 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 116 through 124 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 125 through 138 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 139 through 148 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 149 through 162 )

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