PDB-6fp7: mTFP1/DARPin 1238_E11 complex in space group P6522

ID or keywords:

Entry

Database: PDB / ID: 6fp7

Title

mTFP1/DARPin 1238_E11 complex in space group P6522

Components

DARPin1238_E11
GFP-like fluorescent chromoprotein cFP484

Keywords

DE NOVO PROTEIN / Darpin / protein binder / designed ankyrin repeat protein

Function / homology

Function and homology information

bioluminescence / generation of precursor metabolites and energy
Similarity search - Function

Biological species

Clavularia sp. (invertebrata)
synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.576 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 2.0	Sep 1, 2021	Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Source and taxonomy / Structure summary Category: chem_comp / database_2 ...chem_comp / database_2 / entity / entity_src_gen / pdbx_struct_mod_residue / struct_conn / struct_ref / struct_ref_seq / struct_ref_seq_dif Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _struct_conn.pdbx_leaving_atom_flag / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end
Revision 3.0	Nov 15, 2023	Group: Atomic model / Data collection Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id
Revision 3.1	Jan 17, 2024	Group: Refinement description / Category: pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6fp7.cif.gz	256.5 KB	Display	PDBx/mmCIF format
PDB format	pdb6fp7.ent.gz	211 KB	Display	PDB format
PDBx/mmJSON format	6fp7.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/6fp7 ftp://data.pdbj.org/pub/pdb/validation_reports/fp/6fp7	HTTPS FTP

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Related structure data

Related structure data	6fp8C 6fp9C 6fpaC 6fpbC 2hqkS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6ksv-2 1rho-4 6a18-d 1cqx-2 6yp4-1 2y7r-1 2vor-d 1bed-1 5jkv-d 3qi8-2 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&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) #174 - Jun 2014 GFP-like Proteins similarity (4) #42 - Jun 2003 Green Fluorescent Protein similarity (4)

Deposited unit

A: GFP-like fluorescent chromoprotein cFP484

B: DARPin1238_E11

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	99.050, 99.050, 214.596
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	179
Space group name H-M	P6₅22

Components on special symmetry positions

ID	Model	Components
1	1	A-573- HOH
2	1	A-809- HOH
3	1	B-526- HOH
4	1	B-582- HOH

#1: Protein	GFP-like fluorescent chromoprotein cFP484 Mass: 28546.164 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: PIA is the cofator of mTFP1, it is covalently linked to the protein chain and made o AYG Source: (gene. exp.) Clavularia sp. (invertebrata) / Plasmid: pRSFDUET-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9U6Y3
#2: Protein	DARPin1238_E11 Mass: 17498.865 Da / Num. of mol.: 1 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
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 730 / 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: 3.3 Å³/Da / Density % sol: 62.71 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1 M imidazole pH 7.0 and 30% MPD

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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: 1.576→45.486 Å / Num. obs: 161477 / % possible obs: 99.3 % / Redundancy: 13.5 % / CC_1/2: 0.999 / R_rim(I) all: 0.144 / Net I/σ(I): 13.6
Reflection shell	Resolution: 1.576→1.67 Å / Redundancy: 12.9 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 25309 / CC_1/2: 0.572 / R_rim(I) all: 1.98 / % possible all: 96.4

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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: 2HQK

2hqk

Resolution: 1.576→45.486 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 16.74 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1639	8068	5 %
R_work	0.1478	-	-
obs	0.1486	161477	99.34 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.576→45.486 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3055	0	24	732	3811

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	3182
X-RAY DIFFRACTION	f_angle_d	0.917	4309
X-RAY DIFFRACTION	f_dihedral_angle_d	11.614	1917
X-RAY DIFFRACTION	f_chiral_restr	0.143	473
X-RAY DIFFRACTION	f_plane_restr	0.006	571

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 (%)
1.5762-1.5941	0.3451	222	0.3251	4232	X-RAY DIFFRACTION	82
1.5941-1.6129	0.3083	274	0.2963	5113	X-RAY DIFFRACTION	100
1.6129-1.6325	0.293	270	0.2773	5166	X-RAY DIFFRACTION	100
1.6325-1.6532	0.29	268	0.2642	5165	X-RAY DIFFRACTION	100
1.6532-1.675	0.2598	271	0.255	5151	X-RAY DIFFRACTION	100
1.675-1.6979	0.2583	271	0.2433	5089	X-RAY DIFFRACTION	100
1.6979-1.7222	0.2182	271	0.2304	5155	X-RAY DIFFRACTION	100
1.7222-1.7479	0.2362	277	0.217	5152	X-RAY DIFFRACTION	100
1.7479-1.7752	0.2352	272	0.2152	5153	X-RAY DIFFRACTION	100
1.7752-1.8043	0.23	269	0.2081	5180	X-RAY DIFFRACTION	100
1.8043-1.8354	0.2041	268	0.2105	5145	X-RAY DIFFRACTION	100
1.8354-1.8688	0.2129	270	0.2171	5137	X-RAY DIFFRACTION	100
1.8688-1.9047	0.1998	272	0.1919	5118	X-RAY DIFFRACTION	100
1.9047-1.9436	0.1858	272	0.1645	5125	X-RAY DIFFRACTION	100
1.9436-1.9859	0.1864	273	0.1555	5175	X-RAY DIFFRACTION	100
1.9859-2.0321	0.17	274	0.144	5110	X-RAY DIFFRACTION	100
2.0321-2.0829	0.1589	269	0.1427	5151	X-RAY DIFFRACTION	100
2.0829-2.1392	0.1653	266	0.1399	5145	X-RAY DIFFRACTION	100
2.1392-2.2021	0.1463	273	0.1268	5180	X-RAY DIFFRACTION	100
2.2021-2.2732	0.1593	274	0.1383	5126	X-RAY DIFFRACTION	100
2.2732-2.3545	0.1612	266	0.1362	5148	X-RAY DIFFRACTION	100
2.3545-2.4487	0.1561	271	0.1331	5146	X-RAY DIFFRACTION	100
2.4487-2.5602	0.1514	270	0.13	5156	X-RAY DIFFRACTION	100
2.5602-2.6951	0.1567	268	0.1342	5086	X-RAY DIFFRACTION	99
2.6951-2.8639	0.1648	268	0.1347	5155	X-RAY DIFFRACTION	100
2.8639-3.085	0.1619	278	0.1338	5166	X-RAY DIFFRACTION	100
3.085-3.3954	0.1452	272	0.13	5145	X-RAY DIFFRACTION	100
3.3954-3.8865	0.1212	265	0.121	5141	X-RAY DIFFRACTION	100
3.8865-4.8957	0.1228	263	0.1094	5159	X-RAY DIFFRACTION	100
4.8957-45.5045	0.1649	271	0.1538	5139	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	1.0202	-0.277	1.9334	1.3067	-0.6743	3.9174	-0.0423	-0.8401	0.3955	1.0032	-0.0594	-1.029	-1.017	0.4488	0.2016	0.671	-0.0877	0.0603	0.4693	-0.092	0.4801	67.0508	42.3274	242.2506
2	0.9538	-0.0496	-0.4584	1.2795	0.5428	4.6867	0.0509	0.0128	0.0998	0.0915	-0.0828	0.2319	-0.1328	-0.4353	-0.0091	0.1621	-0.0111	-0.0052	0.1683	-0.008	0.2302	60.9175	32.3469	218.6095
3	0.7151	0.8093	0.7783	0.9578	0.2392	3.5382	0.0708	-0.19	0.1986	0.1458	-0.1439	0.1907	0.0497	-0.4299	-0.0029	0.1911	-0.0207	0.0317	0.2108	-0.0293	0.2356	60.9921	30.3203	226.762
4	0.7816	0.1409	0.1576	1.1606	0.0304	1.5061	0.0648	-0.062	0.0774	0.1337	-0.0769	0.0179	-0.0359	0.0402	0.0192	0.156	-0.0264	-0.0044	0.1411	0.0072	0.1636	72.2482	33.3199	223.6671
5	2.5605	-1.1309	-1.9908	3.2734	1.4382	4.895	0.135	0.0008	0.2633	0.0581	-0.0748	0.3505	-0.5071	-0.1691	-0.0871	0.1621	0.0019	0.0054	0.1452	-0.0185	0.2347	66.1114	39.7267	221.5589
6	1.1969	-0.1569	-0.5874	1.5504	0.3203	2.5372	0.043	0.0596	0.018	-0.0992	-0.0531	0.0595	0.1281	-0.0501	0.0155	0.1725	-0.004	-0.0383	0.1555	-0.0016	0.1745	68.7184	27.0441	212.8732
7	1.1686	0.751	0.1529	1.4283	0.3933	0.7022	-0.0116	0.0202	0.0621	0.0358	-0.0547	0.0302	0.001	0.1889	0.0248	0.1984	-0.0319	-0.0383	0.1931	0.0388	0.1899	80.3516	30.1678	225.0885
8	1.4725	1.2397	0.3423	5.1252	1.5324	1.5523	0.0321	-0.0071	-0.1317	0.1393	-0.0186	-0.3156	0.1082	0.2157	0.0316	0.2137	-0.0291	-0.0402	0.1933	0.0355	0.1879	80.2925	27.2722	222.4605
9	1.3216	0.3544	0.0498	1.7899	0.0483	1.6799	0.069	-0.0205	0.042	0.0739	-0.1366	-0.0893	-0.1022	0.1437	0.044	0.1624	-0.0297	-0.0243	0.1641	0.0297	0.1704	79.3235	33.6668	223.8795
10	3.434	1.5393	0.8743	2.1012	-0.3042	1.834	0.1297	-0.1518	-0.0811	0.0738	-0.0981	0.0682	0.2911	-0.1137	-0.091	0.2017	-0.0247	0.0023	0.1577	-0.0006	0.1754	66.8308	22.4047	225.2597
11	1.7601	1.8632	-0.5074	3.2483	0.5322	2.0363	0.3139	-0.4876	-0.1636	0.4151	-0.2513	-0.1825	0.1323	0.0468	-0.0106	0.2567	-0.0512	-0.0056	0.1991	0.0141	0.1622	73.1765	27.7123	232.749
12	0.6705	-1.196	-1.4408	2.4118	2.2812	3.8272	-0.14	0.0902	0.1916	0.5496	0.0971	-0.7748	0.1783	0.9149	-0.2248	0.4383	-0.1854	-0.2152	0.405	0.1303	0.4801	84.6751	50.7437	211.9016
13	2.2992	1.6878	-0.8298	2.6169	-0.4625	0.4281	-0.2619	0.0865	0.7027	-0.0469	-0.2027	-0.7271	-0.5293	0.4175	0.0672	0.675	-0.339	-0.3836	0.3159	0.1246	0.7803	82.4823	60.8773	212.2099
14	1.2845	0.2956	-0.5948	1.2229	-0.2819	1.5233	0.0892	0.2244	0.4197	-0.0175	-0.3567	-0.2834	-0.2858	0.5404	0.1551	0.2501	-0.074	-0.0525	0.3329	0.1377	0.3512	81.5506	47.8336	207.257
15	2.8404	-0.0613	0.0417	3.9022	-0.2269	2.7128	-0.2577	-0.2045	0.551	0.2048	-0.1471	-0.3983	-0.72	0.1433	0.3018	0.3918	-0.0759	-0.141	0.2422	0.0428	0.3296	73.2944	57.1705	207.4474
16	1.2421	-0.0692	0.806	1.9966	-0.4341	1.2939	-0.0433	-0.0427	0.1263	0.0445	-0.1727	-0.1958	-0.2304	0.0963	0.1492	0.2281	-0.0149	-0.0349	0.216	0.0328	0.2117	69.0577	48.4461	204.7328
17	5.8947	-0.8409	-0.807	2.2762	1.5394	6.3724	-0.3039	0.0258	1.0379	-0.3244	-0.1218	0.127	-1.1524	0.0529	0.3437	0.3789	0.014	-0.0979	0.1647	0.003	0.3425	64.7493	59.0524	201.3302
18	0.3407	-0.4121	0.402	4.0672	-2.5689	2.3646	0.0926	0.0735	-0.0753	0.0038	-0.0977	-0.0745	-0.1077	0.0362	-0.0078	0.1981	0.0153	-0.0193	0.1945	0.0165	0.1934	63.2698	43.7406	199.7525
19	2.8539	-0.3016	0.1691	1.7731	1.314	3.4088	0.055	-0.5657	-0.1493	0.4119	-0.0621	-0.1278	0.0872	-0.5575	0.0384	0.2422	0.0428	-0.0054	0.2958	0.0236	0.1748	56.1377	47.709	207.6451
20	5.8632	-0.7291	-0.6465	2.4552	0.4455	7.3786	-0.0706	-0.3212	0.6504	0.2192	0.1824	-0.1529	-0.6621	-0.1063	-0.0072	0.2713	0.0776	-0.0133	0.2025	-0.0199	0.2521	54.9189	55.8744	200.1862
21	1.7682	-0.4632	0.4123	5.0641	-2.6186	3.7688	0.0377	-0.1682	-0.2827	-0.2628	0.0085	0.1359	0.1466	-0.324	-0.0301	0.1681	0.0095	0.0037	0.2229	0.0349	0.2346	54.3371	39.2118	199.5733
22	3.1356	-0.537	-1.2283	1.3464	0.3623	1.8811	-0.1057	-0.7529	-0.3486	0.4061	0.1857	-0.0327	-0.1034	-0.0039	-0.0374	0.2389	0.0886	0.037	0.3933	0.0846	0.2106	48.3243	43.9639	208.3232
23	1.4335	-0.0834	2.3049	0.7795	-1.6075	7.7906	-0.1417	0.0362	0.0272	-0.0639	0.0145	0.1448	-0.0825	-0.187	0.1043	0.2071	0.0859	0.0369	0.292	-0.0017	0.1913	43.9526	49.5904	199.3064

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid -7 through 7 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 8 through 32 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 33 through 46 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 47 through 99 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 100 through 112 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 113 through 135 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 136 through 151 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 152 through 163 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 164 through 188 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 189 through 205 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 206 through 220 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 2 through 15 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 16 through 27 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 28 through 41 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 42 through 60 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 61 through 84 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 85 through 93 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 94 through 107 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 108 through 117 )
20	X-RAY DIFFRACTION	20	chain 'B' and (resid 118 through 127 )
21	X-RAY DIFFRACTION	21	chain 'B' and (resid 128 through 140 )
22	X-RAY DIFFRACTION	22	chain 'B' and (resid 141 through 150 )
23	X-RAY DIFFRACTION	23	chain 'B' and (resid 151 through 164 )

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The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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