PDB-5ma3: GFP-binding DARPin fusion gc_R11

ID or keywords:

Entry

Database: PDB / ID: 5ma3

Title

GFP-binding DARPin fusion gc_R11

Components

Green fluorescent protein
R11

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: 1.7 Å

Authors

Hansen, S. / Stueber, J. / Ernst, P. / 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 / Database references Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 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
Revision 2.1	Oct 23, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5ma3.cif.gz	311.6 KB	Display	PDBx/mmCIF format
PDB format	pdb5ma3.ent.gz	255.9 KB	Display	PDB format
PDBx/mmJSON format	5ma3.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	5ma3_validation.pdf.gz	447.8 KB	Display	wwPDB validaton report
Full document	5ma3_full_validation.pdf.gz	449.3 KB	Display
Data in XML	5ma3_validation.xml.gz	24.2 KB	Display
Data in CIF	5ma3_validation.cif.gz	36 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ma/5ma3 ftp://data.pdbj.org/pub/pdb/validation_reports/ma/5ma3	HTTPS FTP

-
Related structure data

Related structure data	5ma4C 5ma5C 5ma6C 5ma8C 5ma9C 5madC 5makC C: citing same article (ref.)
Similar structure data	5ma9-1 5mak-2 5mak-1 5ma9-2 2vxb-d 4ms6-d 6enb-d 4dpr-d 5nia-d 6enc-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

-
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: R11

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	59.850, 90.610, 60.920
Angle α, β, γ (deg.)	90.00, 103.42, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Green fluorescent protein Mass: 27453.949 Da / Num. of mol.: 1 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	R11 Mass: 31647.250 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli K-12 (bacteria)
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 393 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.72 Å³/Da / Density % sol: 54.74 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 0.2 M Sodium Acetate, 0.1 M Sodium Cacodylate pH 6.5, 30% w/v PEG 8000

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS3 S 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: 1.7→48.979 Å / Num. obs: 67771 / % possible obs: 97.6 % / Redundancy: 6.7 % / CC_1/2: 0.997 / R_merge(I) obs: 0.105 / Net I/σ(I): 10.47
Reflection shell	Resolution: 1.7→1.74 Å / Redundancy: 6.9 % / R_merge(I) obs: 3.44 / Mean I/σ(I) obs: 0.98 / CC_1/2: 0.561 / % possible all: 98.6

-
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: 1.7→48.979 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.91 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1916	3255	4.8 %
R_work	0.1612	-	-
obs	0.1627	67771	97.6 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.7→48.979 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4057	0	24	393	4474

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	4183
X-RAY DIFFRACTION	f_angle_d	0.851	5665
X-RAY DIFFRACTION	f_dihedral_angle_d	14.153	2441
X-RAY DIFFRACTION	f_chiral_restr	0.052	627
X-RAY DIFFRACTION	f_plane_restr	0.005	747

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 (%)
1.7-1.7254	0.3507	175	0.3394	2741	X-RAY DIFFRACTION	97
1.7254-1.7523	0.356	135	0.3114	2843	X-RAY DIFFRACTION	98
1.7523-1.7811	0.3337	133	0.3063	2803	X-RAY DIFFRACTION	98
1.7811-1.8118	0.3142	160	0.2772	2778	X-RAY DIFFRACTION	98
1.8118-1.8447	0.3456	131	0.259	2828	X-RAY DIFFRACTION	99
1.8447-1.8802	0.3309	144	0.2569	2809	X-RAY DIFFRACTION	98
1.8802-1.9186	0.2887	150	0.2414	2772	X-RAY DIFFRACTION	98
1.9186-1.9603	0.2427	139	0.2149	2824	X-RAY DIFFRACTION	98
1.9603-2.0059	0.2693	115	0.1965	2733	X-RAY DIFFRACTION	95
2.0059-2.0561	0.1948	126	0.1836	2843	X-RAY DIFFRACTION	98
2.0561-2.1117	0.2158	127	0.1766	2815	X-RAY DIFFRACTION	99
2.1117-2.1738	0.2242	142	0.1696	2859	X-RAY DIFFRACTION	99
2.1738-2.244	0.2143	150	0.1622	2793	X-RAY DIFFRACTION	98
2.244-2.3242	0.1902	112	0.1595	2873	X-RAY DIFFRACTION	98
2.3242-2.4172	0.1944	194	0.1535	2775	X-RAY DIFFRACTION	98
2.4172-2.5272	0.2018	146	0.1529	2828	X-RAY DIFFRACTION	99
2.5272-2.6605	0.1762	164	0.1504	2797	X-RAY DIFFRACTION	98
2.6605-2.8272	0.2137	145	0.1537	2723	X-RAY DIFFRACTION	96
2.8272-3.0454	0.1862	123	0.1565	2820	X-RAY DIFFRACTION	97
3.0454-3.3518	0.1907	144	0.1526	2836	X-RAY DIFFRACTION	98
3.3518-3.8367	0.1688	139	0.1365	2779	X-RAY DIFFRACTION	97
3.8367-4.8331	0.1338	145	0.1171	2788	X-RAY DIFFRACTION	96
4.8331-48.9991	0.1568	116	0.1571	2856	X-RAY DIFFRACTION	96

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	8.8253	0.711	1.8431	6.0295	-0.2725	2.6131	0.0807	0.1651	-1.3499	-0.376	-0.5212	0.2858	1.5221	-0.9167	0.0582	0.473	-0.0853	-0.0194	0.2775	-0.0751	0.5565	67.2471	-22.1656	14.864
2	2.6263	3.3551	-2.3775	5.6257	-1.3636	7.6355	-0.0168	0.0315	-0.1689	-0.1997	-0.0259	-0.362	0.0061	0.3529	0.1498	0.0737	0.0416	-0.0161	0.3088	-0.0192	0.285	81.1927	-1.6233	11.1208
3	7.3939	4.8619	-2.6659	5.4043	-3.7092	3.5848	-0.0031	-0.2963	-0.2481	0.0324	-0.1455	-0.275	0.0123	0.3155	0.1414	0.2647	0.0272	0.0149	0.2439	-0.0774	0.2637	76.7433	-4.5338	17.1582
4	1.9256	-0.2384	-0.0871	1.1306	-0.5223	1.6792	-0.0259	-0.0665	-0.0445	0.0086	-0.0251	-0.2778	-0.1069	0.1853	0.0517	0.2459	-0.0003	0.0009	0.2887	-0.022	0.2774	77.26	2.4709	16.7781
5	8.7243	2.6237	1.9415	2.5707	0.4321	3.325	0.0084	-0.225	-0.7897	-0.1961	0.0844	0.0581	0.2822	-0.2528	-0.1259	0.2642	-0.0101	-0.0334	0.2363	0.0041	0.3701	60.0818	-14.2417	12.2008
6	1.6814	0.3239	0.1791	2.7058	-0.2013	1.3268	-0.0392	0.1381	-0.042	-0.174	0.0005	-0.1476	0.0419	0.1466	0.0387	0.1986	0.0057	0.0146	0.273	-0.0438	0.2048	73.719	0.5515	7.6439
7	5.1231	-0.7526	-0.7361	7.3444	3.36	8.227	-0.082	0.6395	-0.5955	-0.6911	0.0299	-0.1591	0.2312	0.1416	0.0623	0.2788	-0.0322	0.0122	0.3162	-0.0659	0.3019	60.3879	-6.013	1.0163
8	2.721	-0.7782	-0.0527	7.7026	2.5244	3.634	-0.035	0.1769	0.1288	-0.2787	-0.0951	0.1765	-0.1647	-0.0756	0.1488	0.1866	-0.0014	-0.0019	0.2587	-0.005	0.194	65.3369	4.1918	6.2914
9	2.9688	0.4718	0.9105	0.935	-0.6703	1.0505	0.0276	0.1851	-0.2985	-0.2028	0.0418	0.0108	0.1932	0.0402	-0.0434	0.2408	0.0037	-0.0137	0.2111	-0.0373	0.3225	62.9236	-9.3695	8.1581
10	4.0879	-0.011	-0.0635	3.5733	-1.9328	7.5271	0.1059	-0.4237	-0.3104	0.4948	-0.257	-0.3681	-0.0777	0.5228	0.0827	0.3019	-0.0344	-0.0615	0.3699	-0.0055	0.3014	81.5201	4.4432	26.6762
11	5.0413	3.9399	5.2175	3.0986	4.0715	5.3996	0.0891	-0.0602	-0.3405	0.0251	0.0018	0.1015	0.2275	-0.1022	-0.1291	0.2448	-0.0134	-0.0257	0.2492	0.0006	0.2992	61.1427	-6.199	16.9377
12	2.4761	-0.8342	0.7591	1.7566	-0.5748	1.4711	-0.1022	-0.2489	-0.2606	0.1392	0.1813	0.0478	-0.0056	-0.3433	-0.0732	0.2235	0.0253	0.0182	0.3183	0.0365	0.1957	63.4638	-10.507	35.7556
13	3.4808	-0.7792	0.3939	2.0392	0.5092	3.1191	-0.0128	-0.1691	-0.0477	-0.0053	0.0476	0.0797	-0.0887	-0.1536	-0.0295	0.2205	0.0023	-0.0264	0.2754	-0.0027	0.3283	43.398	1.3355	7.6913
14	3.6056	-0.6795	-0.7556	3.5758	0.0503	3.7628	0.0957	0.3683	-0.0389	-0.4531	-0.066	0.0148	-0.194	-0.0031	-0.0163	0.3505	0.0092	-0.0395	0.33	-0.0189	0.2762	48.1941	0.6857	-11.5959

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'B' and (resid 1 through 11 )
2	X-RAY DIFFRACTION	2	chain 'B' and (resid 12 through 24 )
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 25 through 39 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 40 through 64 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 68 through 81 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 82 through 147 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 148 through 158 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 159 through 187 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 188 through 208 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 209 through 218 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 219 through 230 )
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 9 through 177 )
13	X-RAY DIFFRACTION	13	chain 'A' and (resid 178 through 256 )
14	X-RAY DIFFRACTION	14	chain 'A' and (resid 257 through 310 )

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi