PDB-5ma5: GFP-binding DARPin fusion gc_K11

ID or keywords:

Entry

Database: PDB / ID: 5ma5

Title

GFP-binding DARPin fusion gc_K11

Components

Green fluorescent protein
K11

Keywords

FLUORESCENT PROTEIN / green fluorescent protein / designed ankyrin protein

Function / homology

Function and homology information

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

Biological species

Aequorea victoria (jellyfish)
synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.85 Å

Authors

Hansen, S. / Stueber, J. / Ernst, P. / Koch, A. / Bojar, D. / Batyuk, A. / Plueckthun, A.

Citation

Journal: Sci Rep / Year: 2017
Title: Design and applications of a clamp for Green Fluorescent Protein with picomolar affinity.
Authors: Hansen, S. / Stuber, J.C. / Ernst, P. / Koch, A. / Bojar, D. / Batyuk, A. / Pluckthun, A.

History

Deposition	Nov 3, 2016	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Nov 8, 2017	Provider: repository / Type: Initial release
Revision 1.1	Dec 6, 2017	Group: Database references / Category: citation / citation_author 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.name
Revision 2.0	Nov 15, 2023	Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Revision 2.1	Nov 13, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5ma5.cif.gz	603.4 KB	Display	PDBx/mmCIF format
PDB format	pdb5ma5.ent.gz	509.1 KB	Display	PDB format
PDBx/mmJSON format	5ma5.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/ma/5ma5 ftp://data.pdbj.org/pub/pdb/validation_reports/ma/5ma5	HTTPS FTP

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Related structure data

Related structure data	5ma3C 5ma4C 5ma6C 5ma8C 5ma9C 5madC 5makC C: citing same article (ref.)
Similar structure data	5ma9-2 5ma9-3 4mxa-d 3umg-4 5mak-2 5ma9-1 6bfa-d 4mx9-d 3ku2-d 1sz9-d 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 - 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	#174 - Jun 2014 GFP-like Proteins similarity (5) #42 - Jun 2003 Green Fluorescent Protein similarity (6) #70 - Oct 2005 Designer Proteins similarity (1)

Deposited unit

B: Green fluorescent protein

A: K11

D: Green fluorescent protein

C: K11

hetero molecules

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

1

B: Green fluorescent protein

A: K11

hetero molecules

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

2

D: Green fluorescent protein

C: K11

hetero molecules

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

Unit cell

Length a, b, c (Å)	58.710, 60.280, 90.240
Angle α, β, γ (deg.)	86.94, 79.13, 89.35
Int Tables number	1
Space group name H-M	P1

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Protein , 2 types, 4 molecules BDAC

#1: Protein	Green fluorescent protein Mass: 27453.949 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P42212
#2: Protein	K11 Mass: 31635.191 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli K-12 (bacteria)

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Non-polymers , 5 types, 790 molecules

#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-CIT / CITRIC ACID Mass: 192.124 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₆H₈O₇
#5: Chemical	ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL Mass: 60.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O / Comment: alkaloid*YM
#6: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 779 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.65 Å³/Da / Density % sol: 53.58 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 0.1M tri Sodium citrate pH 5.6, 20% v/v 2-Propanol, 20%w/v PEG 4000

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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: Dec 18, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.85→44.249 Å / Num. obs: 92746 / % possible obs: 89.5 % / Redundancy: 3.74 % / CC_1/2: 0.999 / R_merge(I) obs: 0.044 / Net I/σ(I): 18.31
Reflection shell	Resolution: 1.85→1.9 Å / Redundancy: 3.76 % / R_merge(I) obs: 0.654 / Mean I/σ(I) obs: 2.46 / CC_1/2: 0.808 / % possible all: 89.2

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Processing

Software

Name	Version	Classification
PHENIX	(1.11_2567: ???)	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.85→44.249 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 21.86 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1836	4614	4.97 %
R_work	0.1541	-	-
obs	0.1556	92746	89.52 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.85→44.249 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8018	0	74	779	8871

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	8325
X-RAY DIFFRACTION	f_angle_d	0.859	11288
X-RAY DIFFRACTION	f_dihedral_angle_d	15.396	4882
X-RAY DIFFRACTION	f_chiral_restr	0.053	1250
X-RAY DIFFRACTION	f_plane_restr	0.006	1490

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 (%)
1.85-1.871	0.3142	152	0.2995	2806	X-RAY DIFFRACTION	86
1.871-1.893	0.3197	153	0.2741	3055	X-RAY DIFFRACTION	92
1.893-1.9161	0.2795	180	0.2512	2959	X-RAY DIFFRACTION	91
1.9161-1.9403	0.2578	152	0.2387	2996	X-RAY DIFFRACTION	92
1.9403-1.9659	0.2383	140	0.2218	3015	X-RAY DIFFRACTION	91
1.9659-1.9928	0.257	157	0.217	2983	X-RAY DIFFRACTION	91
1.9928-2.0213	0.2529	149	0.2057	3017	X-RAY DIFFRACTION	91
2.0213-2.0515	0.2545	162	0.2041	2922	X-RAY DIFFRACTION	91
2.0515-2.0835	0.2192	158	0.189	3002	X-RAY DIFFRACTION	90
2.0835-2.1177	0.2385	153	0.1863	2863	X-RAY DIFFRACTION	89
2.1177-2.1542	0.2067	131	0.1823	2941	X-RAY DIFFRACTION	88
2.1542-2.1933	0.2127	157	0.171	2767	X-RAY DIFFRACTION	86
2.1933-2.2355	0.2161	134	0.1738	2623	X-RAY DIFFRACTION	79
2.2355-2.2812	0.1895	170	0.1702	2955	X-RAY DIFFRACTION	91
2.2812-2.3308	0.1972	171	0.1648	3053	X-RAY DIFFRACTION	93
2.3308-2.385	0.1847	143	0.156	3058	X-RAY DIFFRACTION	92
2.385-2.4446	0.1912	169	0.1561	3015	X-RAY DIFFRACTION	92
2.4446-2.5107	0.1793	138	0.1493	3027	X-RAY DIFFRACTION	92
2.5107-2.5846	0.1864	145	0.1524	3013	X-RAY DIFFRACTION	91
2.5846-2.668	0.1665	155	0.1506	2957	X-RAY DIFFRACTION	90
2.668-2.7633	0.1942	132	0.1662	2894	X-RAY DIFFRACTION	88
2.7633-2.874	0.2498	146	0.1637	2671	X-RAY DIFFRACTION	81
2.874-3.0047	0.2138	141	0.1587	3006	X-RAY DIFFRACTION	91
3.0047-3.1631	0.1831	160	0.157	3083	X-RAY DIFFRACTION	94
3.1631-3.3612	0.1865	147	0.1553	3036	X-RAY DIFFRACTION	92
3.3612-3.6206	0.1877	179	0.1471	2940	X-RAY DIFFRACTION	90
3.6206-3.9848	0.1584	175	0.1272	2827	X-RAY DIFFRACTION	87
3.9848-4.5609	0.1302	140	0.1051	2771	X-RAY DIFFRACTION	84
4.5609-5.7442	0.116	169	0.1124	3001	X-RAY DIFFRACTION	92
5.7442-44.2621	0.1626	156	0.1432	2876	X-RAY DIFFRACTION	87

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	1.7985	0.0513	0.7905	1.4329	0.2027	2.5231	0.0442	-0.2987	-0.3019	0.2904	-0.0211	0.0578	0.022	-0.2245	0.1553	0.2673	-0.0003	0.0314	0.2224	0.0434	0.2492	-3.8284	-76.6937	5.9719
2	1.553	0.3299	0.7804	1.9003	0.7839	1.9572	0.1325	-0.008	-0.3525	0.0227	-0.0544	0.0053	0.17	-0.0572	-0.0719	0.2078	-0.0172	0.0157	0.181	-0.0005	0.2806	-0.2053	-77.95	-3.845
3	2.9964	-1.3279	-0.5969	5.5306	0.2583	2.0751	-0.0217	-0.3195	0.1416	0.2834	0.0599	-0.0953	-0.0701	0.0822	0.018	0.2538	-0.0003	0.0155	0.2675	-0.007	0.2122	-0.2648	-61.1737	11.1089
4	1.2746	-0.0178	0.5627	0.9867	0.2899	2.3681	0.0497	-0.2176	-0.1984	0.1903	-0.0445	0.1308	0.1258	-0.1879	-0.0071	0.2297	-0.0331	0.041	0.2243	0.0369	0.2543	-10.1908	-73.433	1.0773
5	1.2018	0.1599	0.4839	0.996	-0.2435	0.7194	0.0377	0.1055	-0.0331	-0.0407	-0.0208	0.0938	-0.0106	-0.1609	0.0307	0.2022	-0.0114	0.0345	0.2132	-0.0231	0.2198	-8.689	-66.6278	-7.1732
6	2.2075	0.005	-2.1952	1.4824	-0.0834	6.2767	0.0654	0.2477	0.0309	-0.2064	-0.0802	-0.1602	-0.1071	-0.0899	0.0633	0.2508	-0.0104	0.0385	0.2162	-0.0066	0.2472	-4.2857	-64.0412	-11.0398
7	0.7559	0.0241	0.2873	2.1688	-1.4959	3.9313	-0.1088	-0.0347	0.0797	0.022	0.0337	0.2298	-0.1904	-0.2312	-0.0896	0.1927	0.0071	0.0192	0.2102	0.0001	0.2204	-10.7791	-65.3232	-5.2386
8	1.6521	-0.3237	-0.1551	1.8003	0.4449	0.9499	0.0234	-0.068	-0.0889	0.154	0.0055	-0.1035	0.0465	-0.0698	-0.0358	0.2068	-0.009	-0.0046	0.1995	0.0039	0.1888	0.9531	-69.0451	1.1301
9	0.5509	-0.5007	0.5617	1.2843	-0.2477	1.6925	0.2449	-0.1469	-0.3236	0.3415	-0.0302	-0.1768	0.6436	0.0508	-0.1513	0.4963	0.0258	-0.1317	0.287	0.0182	0.4431	22.6465	-85.0859	12.6015
10	1.1135	0.1418	-0.1507	1.6535	-0.0446	1.1001	0.0438	-0.0755	0.1098	0.1141	0.0083	-0.2369	-0.0001	0.0989	-0.0469	0.1967	0.0008	-0.0017	0.2152	-0.0227	0.2875	20.5129	-62.7093	4.3573
11	1.8385	-0.1403	-0.1032	2.1574	0.0051	1.7673	-0.0869	-0.0635	0.1998	-0.0406	-0.0436	-0.1211	-0.0926	0.1992	0.1056	0.2354	-0.0057	0.009	0.186	0.0035	0.2923	-1.547	-43.6201	-4.2443
12	1.7326	0.3689	-0.0877	2.1962	-0.152	1.9265	-0.0217	-0.0517	0.1191	0.0785	-0.0049	0.3294	-0.0206	-0.269	0.0265	0.2117	0.015	0.0002	0.2376	-0.0274	0.361	-21.4024	-45.1374	-3.3834
13	2.8116	-0.0986	1.5547	1.1307	-0.062	1.922	0.0245	0.2023	0.053	-0.2703	-0.0353	-0.1888	0.0053	0.3669	0.0213	0.4266	-0.0621	-0.0962	0.3913	0.0665	0.468	29.0549	-75.7595	-48.0412
14	1.6382	-0.5943	0.7132	0.7111	-0.0438	1.5624	-0.1295	-0.032	0.1695	-0.1998	0.027	0.12	-0.2553	0.077	0.0415	0.4012	-0.0594	-0.1328	0.2944	0.0664	0.3631	18.3128	-74.2998	-46.2937
15	4.5205	-2.3809	-1.5661	6.8542	2.8137	3.2788	0.1884	-0.1495	-0.2375	-0.0099	0.08	-0.1841	0.4205	0.4751	-0.1195	0.4455	0.0179	-0.1955	0.4143	0.0753	0.4952	33.5725	-90.5609	-42.9057
16	1.6697	-0.4083	0.4593	0.922	0.0764	1.6976	0.0707	0.025	0.1414	-0.1549	-0.047	0.0093	-0.0622	-0.0342	-0.0204	0.4168	-0.0637	-0.1129	0.3008	0.078	0.3562	18.9082	-79.8047	-53.7981
17	2.8579	0.3047	0.3857	1.8447	0.2104	1.0392	0.0185	0.1053	-0.1576	-0.1567	0.0205	-0.0407	0.3022	0.0796	-0.0144	0.4785	-0.0157	-0.1314	0.324	0.0622	0.348	22.7789	-89.6668	-54.1334
18	1.0417	-0.4072	-0.0006	1.2046	0.1942	1.1849	0.0116	-0.2242	0.0121	0.1556	-0.0575	0.0412	0.073	-0.1362	-0.0245	0.3757	-0.0344	-0.1438	0.3515	0.0526	0.3506	18.6101	-80.5973	-40.3542
19	2.081	1.1264	1.3743	1.3157	1.2579	1.8422	-0.1473	-0.0835	0.4144	-0.2565	-0.0715	0.1071	-0.141	-0.084	0.004	0.3033	0.0044	-0.0539	0.3435	-0.0215	0.3413	29.6635	-61.3718	-22.7169
20	1.587	0.5651	0.588	1.3749	-0.0754	1.2028	0.1775	-0.3565	-0.2933	0.0187	0.0321	-0.0155	0.3961	-0.3119	-0.1089	0.3226	-0.0814	-0.0747	0.3896	0.0748	0.308	24.6694	-84.2007	-22.688
21	0.3967	0.3731	-0.2029	0.775	0.2378	0.5287	-0.0911	-0.6197	-0.5974	0.1007	0.0287	0.4171	0.697	0.2202	-0.0705	0.8341	-0.0539	-0.2226	0.5793	0.3003	0.7383	19.9615	-107.7384	-38.8501
22	0.9985	-0.375	0.0713	1.0124	0.1581	0.0423	0.403	0.0438	-0.6969	-0.4302	-0.0582	0.279	0.6677	0.1912	0.4158	1.0332	0.0875	-0.3584	0.2506	0.0795	0.7147	20.7641	-108.7062	-57.8217

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'B' and (resid 2 through 24 )
2	X-RAY DIFFRACTION	2	chain 'B' and (resid 25 through 68 )
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 69 through 81 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 82 through 128 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 129 through 159 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 160 through 175 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 176 through 187 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 188 through 231 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 13 through 68 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 69 through 177 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 178 through 256 )
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 257 through 310 )
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 2 through 24 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 25 through 68 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 69 through 81 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 82 through 148 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 149 through 198 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 199 through 230 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 11 through 49 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 50 through 168 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 169 through 209 )
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 210 through 309 )

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