PDB-5mak: GFP-binding DARPin fusion gc_R7

ID or keywords:

Entry

Database: PDB / ID: 5mak

Title

GFP-binding DARPin fusion gc_R7

Components

Green fluorescent protein
R7

Keywords

FLUORESCENT PROTEIN / green fluorescent protein / designed ankyrin repeat 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: 2.5 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: Advisory / Atomic model ...Advisory / 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_validate_close_contact / 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_validate_close_contact.auth_atom_id_2 / _struct_conn.pdbx_dist_value
Revision 2.1	Nov 20, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5mak.cif.gz	581.1 KB	Display	PDBx/mmCIF format
PDB format	pdb5mak.ent.gz	490.2 KB	Display	PDB format
PDBx/mmJSON format	5mak.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5mak_validation.pdf.gz	443.9 KB	Display	wwPDB validaton report
Full document	5mak_full_validation.pdf.gz	453.4 KB	Display
Data in XML	5mak_validation.xml.gz	29.3 KB	Display
Data in CIF	5mak_validation.cif.gz	44.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ma/5mak ftp://data.pdbj.org/pub/pdb/validation_reports/ma/5mak	HTTPS FTP

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Related structure data

Related structure data	5ma3C 5ma4C 5ma5C 5ma6C 5ma8C 5ma9C 5madC C: citing same article (ref.)
Similar structure data	5ma5-2 5ma3-d 5ma9-1 5ma9-2 6enb-d 4ms6-d 6rpj-1 1ctu-1 5ma5-1 4dpr-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)

Deposited unit

B: Green fluorescent protein

A: R7

D: Green fluorescent protein

C: R7

hetero molecules

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

1

B: Green fluorescent protein

A: R7

hetero molecules

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

2

D: Green fluorescent protein

C: R7

hetero molecules

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

Unit cell

Length a, b, c (Å)	57.960, 61.380, 89.380
Angle α, β, γ (deg.)	93.12, 102.74, 94.76
Int Tables number	1
Space group name H-M	P1

#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	R7 Mass: 31389.018 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)
#3: Chemical	ChemComp-CIT / CITRIC ACID Mass: 192.124 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₆H₈O₇
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 143 / Source method: isolated from a natural source / Formula: H₂O
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: 2.62 Å³/Da / Density % sol: 53.02 %
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: X06DA / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 19, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.5→43.525 Å / Num. obs: 39327 / % possible obs: 95.1 % / Redundancy: 3.5 % / R_merge(I) obs: 0.141 / Net I/σ(I): 8.62
Reflection shell	Resolution: 2.5→2.56 Å / Redundancy: 3.66 % / R_merge(I) obs: 0.86 / Mean I/σ(I) obs: 1.86 / Num. unique all: 22310 / % possible all: 97.2

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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: 2.5→43.525 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 34.98 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.3036	1896	4.83 %
R_work	0.255	-	-
obs	0.2573	39290	95.08 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.5→43.525 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7960	0	65	143	8168

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	8194
X-RAY DIFFRACTION	f_angle_d	0.506	11121
X-RAY DIFFRACTION	f_dihedral_angle_d	14.493	4810
X-RAY DIFFRACTION	f_chiral_restr	0.04	1239
X-RAY DIFFRACTION	f_plane_restr	0.002	1465

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 (%)
2.5-2.5625	0.3898	142	0.3259	2742	X-RAY DIFFRACTION	97
2.5625-2.6318	0.35	145	0.3314	2759	X-RAY DIFFRACTION	97
2.6318-2.7092	0.3586	132	0.3277	2698	X-RAY DIFFRACTION	98
2.7092-2.7967	0.3599	140	0.3091	2753	X-RAY DIFFRACTION	98
2.7967-2.8966	0.3802	152	0.308	2769	X-RAY DIFFRACTION	98
2.8966-3.0125	0.3551	116	0.2869	2728	X-RAY DIFFRACTION	98
3.0125-3.1496	0.3694	161	0.2887	2693	X-RAY DIFFRACTION	97
3.1496-3.3156	0.3389	143	0.2615	2746	X-RAY DIFFRACTION	98
3.3156-3.5233	0.2911	143	0.2568	2724	X-RAY DIFFRACTION	97
3.5233-3.7952	0.4562	85	0.3703	1788	X-RAY DIFFRACTION	63
3.7952-4.1768	0.2478	144	0.2334	2636	X-RAY DIFFRACTION	94
4.1768-4.7805	0.217	140	0.1902	2751	X-RAY DIFFRACTION	98
4.7805-6.0204	0.2589	135	0.2053	2791	X-RAY DIFFRACTION	99
6.0204-43.5312	0.2377	118	0.1966	2816	X-RAY DIFFRACTION	99

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	1.9166	-0.1933	0.1571	3.0414	-0.7584	1.9538	0.0999	0.0632	0.1855	0.1716	0.0745	-0.165	-0.2657	0.073	-0.1681	0.2596	-0.0504	0.1258	0.2202	-0.0741	0.306	-4.5062	30.472	1.5664
2	2.5152	-0.1055	1.607	4.9136	-2.2532	8.8822	-0.129	0.3386	-0.4799	-0.0599	-0.2851	-0.2849	0.2119	0.6342	0.296	0.1814	-0.0021	0.1275	0.1703	-0.0237	0.3851	-0.853	18.6642	-2.1168
3	2.425	-1.4154	0.9333	2.8507	-1.3007	1.6761	0.0563	-0.1695	0.1276	-0.1506	0.0212	-0.3076	-0.1392	-0.2121	-0.0709	0.2398	-0.0936	0.1257	0.1665	-0.0265	0.2852	-7.1622	24.741	2.3977
4	2.7052	-0.4058	-1.114	3.3921	1.2411	2.7745	-0.0308	-0.0538	-0.0808	0.4293	0.0324	0.2456	0.022	-0.218	0.0481	0.309	-0.0128	0.1645	0.2891	-0.0089	0.369	-30.0905	27.6204	10.1137
5	1.1316	-1.3562	0.6357	2.5586	0.3372	3.0543	-0.1906	-0.1896	-0.7832	-0.0841	-0.0957	0.4317	0.4503	-0.3888	0.4439	0.5417	0.0122	0.3734	0.1876	-0.1145	0.8349	-9.0436	0.397	-0.9135
6	5.4281	3.1978	-0.3	3.3631	0.8655	4.2641	-0.0587	0.2706	0.3267	-0.0482	0.0949	0.0042	-0.0728	0.3277	0.0292	0.3088	0.0114	0.1464	0.2919	0.0293	0.6462	7.0028	1.7056	-4.5989
7	2.8973	0.5219	0.5923	5.8408	-2.5094	2.771	-0.4527	-0.358	-0.0957	0.1025	0.2308	-0.6455	0.1516	0.5746	0.1301	0.1984	0.067	0.0837	0.4686	0.0191	0.8024	17.1952	2.5965	1.0173
8	3.8944	1.0646	-2.6231	0.4042	-0.307	3.4064	0.0927	0.3889	0.2032	-0.161	0.0582	0.1858	-0.1754	-0.1776	-0.2276	0.7277	0.0337	0.4073	0.2911	0.0922	0.5999	2.474	25.6692	41.8762
9	1.4585	0.0619	-0.4354	0.057	0.3005	1.8803	-0.061	-0.1476	-0.0823	-0.1595	-0.0058	-0.2086	0.1286	-0.1804	-0.0693	0.4827	-0.0419	0.5799	0.2201	0.0324	0.4545	12.7537	24.9215	44.2652
10	7.2763	-1.1442	1.9324	5.3505	0.5728	2.6539	-0.2616	-0.9277	-0.176	0.5716	-0.1212	0.7682	-0.5484	-0.9371	0.369	0.7341	0.1591	0.3452	0.4261	-0.0685	0.4067	-2.8939	40.7062	47.0744
11	6.5174	2.8825	-3.191	2.3192	-0.2262	3.2973	-0.6433	0.2674	-0.0766	-0.462	0.4591	-0.0503	0.0536	-0.4191	0.1944	0.5235	0.0528	0.2204	0.2803	0.0417	0.4785	6.6323	34.2808	35.414
12	3.4353	0.5674	0.5931	1.982	-1.5767	1.7396	0.3033	0.2168	-0.204	-0.4352	0.0351	0.3996	0.3271	0.0559	0.3967	0.5777	-0.0175	0.2754	0.2411	-0.1251	0.4961	6.5396	25.4278	35.1788
13	1.388	0.2113	1.721	0.5135	0.3535	4.0092	-0.0626	0.2728	-0.1186	-0.1252	0.2549	-0.2662	-0.0204	0.802	0.0342	0.7162	-0.0861	0.4805	0.4278	-0.0074	0.7603	25.7308	31.7356	40.3033
14	7.763	-3.0951	1.7215	3.9675	-0.8806	3.0316	0.6255	0.5452	-0.1149	-0.3216	-0.4205	-0.0764	-0.3993	0.3663	-0.0586	0.7294	0.0646	0.3577	0.22	-0.0571	0.4817	11.7096	41.2228	37.6282
15	0.2514	-0.0986	-0.1243	0.0774	0.233	1.0403	0.0992	-0.0387	-0.1272	-0.1553	-0.001	-0.116	-0.1409	-0.2409	0.3276	0.7113	0.0577	0.555	0.2828	-0.0938	0.5734	8.9869	34.0037	41.8458
16	1.5453	-0.3667	-0.7033	3.1557	0.8238	1.6001	0.4864	0.0391	0.2771	-1.0494	-0.1359	-0.2843	-0.4614	-0.0304	-0.2097	0.4387	-0.0242	0.1337	0.3167	0.037	0.2592	8.2498	35.5229	49.8881
17	5.589	-0.4949	-0.7052	3.7524	-1.5788	5.139	-0.259	-0.0847	-0.4729	-0.2992	0.2351	0.2209	0.6493	-0.0308	0.1836	0.5689	-0.0294	0.4383	0.3782	0.0983	0.8053	-3.1837	11.3554	67.3291
18	3.2638	0.7927	0.2283	5.2274	-0.7428	2.618	0.1956	-0.2609	0.2338	-0.1178	0.045	0.0011	-0.3526	-0.0236	-0.2904	0.3259	-0.0089	0.1926	0.3198	0.0133	0.306	4.2693	27.9568	68.2567
19	5.4604	0.4769	-2.8517	4.2374	-1.355	4.8181	0.687	0.034	0.7045	-0.2318	0.1164	-0.1684	-1.0868	-0.2915	-0.7171	0.6697	-0.0517	0.1946	0.3428	-0.0277	0.5457	7.7921	46.4333	64.1672
20	3.1843	0.3577	0.6974	1.3341	-0.3912	0.4363	-0.0497	-0.3259	0.2846	0.3153	0.0007	0.2824	-0.3998	-0.1007	-0.2314	1.2272	-0.0082	0.5386	0.1489	0.0843	0.6555	10.293	58.79	47.3782
21	2.9898	0.383	1.2618	3.2183	1.1408	2.1136	0.6068	0.4243	-0.1122	-0.4581	-0.3128	-0.3227	0.2302	0.0181	-0.3499	1.115	0.1096	0.3537	0.3838	0.0872	0.611	12.1379	59.625	31.4897
22	5.5364	-4.429	-0.6391	7.6705	1.2091	0.1914	0.1527	0.5615	-0.188	-1.057	-0.2148	0.5606	-0.2285	-0.1395	0.1881	1.4047	0.2525	0.3255	0.4514	0.0191	0.7068	5.1667	58.7414	21.3237

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'B' and (resid 2 through 148 )
2	X-RAY DIFFRACTION	2	chain 'B' and (resid 149 through 175 )
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 176 through 231 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 13 through 168 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 169 through 239 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 240 through 285 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 286 through 305 )
8	X-RAY DIFFRACTION	8	chain 'D' and (resid 2 through 24 )
9	X-RAY DIFFRACTION	9	chain 'D' and (resid 25 through 68 )
10	X-RAY DIFFRACTION	10	chain 'D' and (resid 69 through 81 )
11	X-RAY DIFFRACTION	11	chain 'D' and (resid 82 through 104 )
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 105 through 128 )
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 129 through 148 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 149 through 175 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 176 through 216 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 217 through 230 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 13 through 35 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 36 through 134 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 135 through 168 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 169 through 238 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 239 through 285 )
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 286 through 305 )

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