PDB-6fp8: mTFP1/DARPin 1238_E11 complex in space group C2

ID or keywords:

Entry

Database: PDB / ID: 6fp8

Title

mTFP1/DARPin 1238_E11 complex in space group C2

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: 1.855 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 / 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	6fp8.cif.gz	246.3 KB	Display	PDBx/mmCIF format
PDB format	pdb6fp8.ent.gz	199.5 KB	Display	PDB format
PDBx/mmJSON format	6fp8.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/6fp8 ftp://data.pdbj.org/pub/pdb/validation_reports/fp/6fp8	HTTPS FTP

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Related structure data

Related structure data	6fp7C 6fp9C 6fpaC 6fpbC 2hqkS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4z9m-3 3tzo-1 4pby-2 4j71-1 3e3q-8 4q93-d 5o6h-2 4ufx-2 1se6-2 6o93-d 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

49.3 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)	135.953, 75.012, 48.295
Angle α, β, γ (deg.)	90.00, 90.73, 90.00
Int Tables number	5
Space group name H-M	C121

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Protein , 2 types, 2 molecules AB

#1: Protein	GFP-like fluorescent chromoprotein cFP484 Mass: 28546.164 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: mTFP1, contains cofactor PIA, made out of amino acids 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: 19879.373 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

#1: Protein

GFP-like fluorescent chromoprotein cFP484

Mass: 28546.164 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: mTFP1, contains cofactor PIA, made out of amino acids 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: 19879.373 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

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Non-polymers , 4 types, 419 molecules

#3: Chemical	ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₆H₁₄O₂ / Comment: precipitant*YM
#4: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO₄
#5: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆O₂
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 410 / 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: 2.86 Å³/Da / Density % sol: 57.04 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: 10% PEG4000, 20% Glycerol, and 0.02 M of L-glutamate, glycine, DL-alanine, L-lysin, DL-serin

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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: 1.855→39.607 Å / Num. obs: 78111 / % possible obs: 96.6 % / Redundancy: 2.4 % / CC_1/2: 0.998 / R_rim(I) all: 0.069 / Net I/σ(I): 11.2
Reflection shell	Resolution: 1.855→1.97 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 12129 / CC_1/2: 0.652 / R_rim(I) all: 0.73 / % possible all: 93.1

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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: 1.855→39.607 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.21 / Phase error: 18.14

	R_factor	Num. reflection	% reflection
R_free	0.1764	3897	4.99 %
R_work	0.1483	-	-
obs	0.1498	78111	96.62 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.855→39.607 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3029	0	52	411	3492

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.012	3164
X-RAY DIFFRACTION	f_angle_d	1.301	4284
X-RAY DIFFRACTION	f_dihedral_angle_d	12.163	1877
X-RAY DIFFRACTION	f_chiral_restr	0.066	462
X-RAY DIFFRACTION	f_plane_restr	0.008	564

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 (%)
1.8546-1.8772	0.3119	109	0.3009	2142	X-RAY DIFFRACTION	79
1.8772-1.901	0.2975	142	0.2612	2677	X-RAY DIFFRACTION	97
1.901-1.926	0.2787	141	0.2517	2651	X-RAY DIFFRACTION	97
1.926-1.9524	0.265	136	0.2474	2635	X-RAY DIFFRACTION	97
1.9524-1.9802	0.2298	141	0.2424	2686	X-RAY DIFFRACTION	97
1.9802-2.0098	0.231	144	0.225	2679	X-RAY DIFFRACTION	97
2.0098-2.0412	0.2358	140	0.2056	2652	X-RAY DIFFRACTION	97
2.0412-2.0747	0.2297	135	0.1977	2680	X-RAY DIFFRACTION	97
2.0747-2.1104	0.1897	139	0.1935	2693	X-RAY DIFFRACTION	98
2.1104-2.1488	0.2153	143	0.1739	2678	X-RAY DIFFRACTION	97
2.1488-2.1901	0.2041	139	0.1749	2667	X-RAY DIFFRACTION	97
2.1901-2.2348	0.2113	142	0.1738	2688	X-RAY DIFFRACTION	99
2.2348-2.2834	0.2254	145	0.1649	2701	X-RAY DIFFRACTION	97
2.2834-2.3365	0.2014	137	0.155	2674	X-RAY DIFFRACTION	98
2.3365-2.395	0.186	140	0.1519	2677	X-RAY DIFFRACTION	98
2.395-2.4597	0.1691	140	0.1452	2652	X-RAY DIFFRACTION	98
2.4597-2.5321	0.158	141	0.1523	2699	X-RAY DIFFRACTION	97
2.5321-2.6138	0.2075	131	0.1623	2509	X-RAY DIFFRACTION	92
2.6138-2.7072	0.1676	139	0.1419	2661	X-RAY DIFFRACTION	96
2.7072-2.8156	0.1596	141	0.1389	2671	X-RAY DIFFRACTION	99
2.8156-2.9437	0.1922	142	0.1409	2720	X-RAY DIFFRACTION	99
2.9437-3.0988	0.1751	145	0.1458	2703	X-RAY DIFFRACTION	99
3.0988-3.2929	0.1507	140	0.1302	2704	X-RAY DIFFRACTION	98
3.2929-3.5469	0.1486	144	0.1248	2713	X-RAY DIFFRACTION	98
3.5469-3.9036	0.1346	144	0.1106	2698	X-RAY DIFFRACTION	98
3.9036-4.4678	0.1566	138	0.1113	2652	X-RAY DIFFRACTION	97
4.4678-5.6264	0.1485	133	0.1237	2562	X-RAY DIFFRACTION	93
5.6264-39.616	0.1847	146	0.1664	2690	X-RAY DIFFRACTION	98

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	0.6824	0.1242	-0.1344	0.3017	0.1961	0.1895	0.0027	0.0029	-0.1371	0.0043	0.0469	-0.0167	0.1045	0.0464	0	0.1601	0.0141	0.0023	0.1375	0.0176	0.171	-12.7185	-2.7741	20.1393
2	0.3729	-0.1641	0.0868	0.1859	0.194	0.5118	-0.0282	-0.0253	-0.0153	-0.0129	0.0169	-0.0262	-0.0301	0.0278	-0	0.1561	0.0143	0.0128	0.1534	0.0233	0.146	-15.9005	4.6756	21.5044
3	0.049	0.0365	0.0286	0.0564	0.0664	0.0248	-0.1039	-0.0049	-0.0632	-0.0238	0.1169	0.0787	-0.0033	-0.1721	0	0.2087	0.0165	0.0008	0.1944	0.0365	0.2003	-21.7035	-0.1136	18.906
4	0.0667	-0.0485	-0.1184	0.0143	-0.0279	0.039	0.0427	-0.0133	-0.1037	-0.0863	0.0548	0.0896	0.1186	-0.1131	0	0.2048	-0.0057	-0.0139	0.1638	0.0319	0.1895	-18.1996	-2.7302	18.2881
5	0.0171	0.0029	-0.0019	0.0421	0.0471	0.0454	0.3081	0.3539	0.1167	-0.423	-0.2762	-0.0843	-0.3272	0.2331	0	0.3617	0.0192	0.0356	0.2753	0.0981	0.2221	-12.2212	15.8051	2.9261
6	0.0339	-0.1924	-0.0025	0.1125	0.0343	0.0862	-0.0657	0.0306	0.0597	0.0564	0.0896	-0.0492	-0.1684	-0.0401	0	0.2111	0.0229	0.0002	0.2107	0.0173	0.1992	-19.1505	14.6168	24.9397
7	0.0546	-0.0995	0.0619	0.082	-0.0506	0.007	0.0144	-0.1158	-0.1502	0.0083	-0.1278	-0.0945	-0.2048	-0.0112	-0	0.2565	0.0265	0.029	0.1704	-0.0055	0.1924	-18.1402	16.2046	21.5147
8	0.4807	-0.1059	0.2379	0.2255	0.2898	0.3624	-0.0205	-0.0608	0.078	-0.0857	-0.009	0.1215	-0.0913	-0.1311	-0	0.183	0.036	0.0085	0.1694	0.0232	0.1362	-21.6134	11.6817	24.4881
9	0.2383	-0.0752	0.2719	0.1906	-0.0214	0.1026	0.0599	0.1112	0.0988	-0.0295	-0.0263	-0.1394	-0.1566	-0.045	-0	0.1729	0.0062	0.0161	0.174	0.0115	0.181	-6.4466	8.3605	18.9961
10	0.6071	0.4139	0.3531	0.3854	-0.4561	0.289	0.1084	-0.1846	0.2773	-0.0599	0.1184	-0.1522	-0.3154	0.0265	0	0.1901	0.0257	-0.0066	0.2048	0.0164	0.1802	-10.6381	9.8854	28.9323
11	0.0084	-0.0594	-0.1291	-0.0079	0.1036	0.1333	-0.2731	-0.5774	0.2158	0.9741	-0.1079	0.564	-0.0834	-0.0234	0	0.3469	0.0009	0.2143	0.3848	-0.0095	0.4291	-45.2597	1.71	21.7785
12	-0.0452	0.1626	-0.078	0.0505	0.2059	0.0059	0.0766	-0.0971	0.0909	0.0283	-0.1109	0.0974	0.0026	-0.0787	0	0.2143	-0.0147	-0.0101	0.2589	0.0016	0.2901	-40.6455	-2.347	15.4343
13	0.0917	0.0143	0.0399	0.0335	0.1523	0.1007	0.0365	0.0649	-0.0398	-0.0682	-0.029	0.0039	0.0217	-0.0299	0	0.1723	-0.0152	-0.0422	0.2212	0.0102	0.2714	-34.0769	-4.7852	8.9891
14	0.0107	-0.0049	-0.0111	-0.0128	-0.0045	0.0035	-0.1911	0.1505	-0.1525	-0.0003	-0.2892	0.0043	0.1477	-0.2245	0	0.2335	-0.0806	-0.0057	0.2871	-0.035	0.2982	-39.9658	-15.2833	8.9831
15	0.1506	-0.0283	-0.1226	0.1073	0.1461	0.2497	0.0033	0.073	-0.054	-0.0295	0.0024	0.0419	0.0144	-0.0323	0	0.2133	-0.0299	-0.0415	0.2201	-0.0172	0.2549	-28.9565	-13.2966	4.4457
16	0.0406	-0.0111	0.0148	0.1557	0.0551	0.1063	-0.0261	0.1717	-0.1634	-0.1909	0.0324	-0.131	0.024	0.0036	0	0.2454	-0.0112	-0.0246	0.2295	-0.0573	0.271	-21.0626	-14.3981	0.3405
17	0.0268	0.0647	0.0004	0.0373	0.0036	0.0175	-0.2312	0.2038	-0.2023	0.1572	-0.2163	-0.2135	0.2193	0.0443	-0	0.4175	-0.0504	0.0103	0.2503	-0.0796	0.4687	-25.0232	-24.7265	-4.9844

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 35 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 36 through 99 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 100 through 110 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 111 through 123 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 124 through 135 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 136 through 151 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 152 through 163 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 164 through 188 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 189 through 205 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 206 through 220 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 12 through 37 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 38 through 70 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 71 through 94 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 95 through 103 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 104 through 136 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 137 through 160 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 161 through 178 )

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Yorodumi