PDB-9j11: Structure of mEos3.2 in the green fluorescent state

ID or keywords:

Entry

Database: PDB / ID: 9j11

Title

Structure of mEos3.2 in the green fluorescent state

Components

Green to red photoconvertible GFP-like protein EosFP

Keywords

FLUORESCENT PROTEIN / Green-to-red photoconvertible fluorescent protein

Function / homology

Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / generation of precursor metabolites and energy / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / Green to red photoconvertible GFP-like protein EosFP

Function and homology information

Biological species

Lobophyllia hemprichii (invertebrata)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.85 Å

Authors

Zheng, S.P. / Shi, X.R.

Funding support

1items

Citation

Journal: Acta Crystallogr D Struct Biol / Year: 2025
Title: Structural basis for the fast maturation of pcStar, a photoconvertible fluorescent protein.
Authors: Zheng, S. / Shi, X. / Lin, J. / Yang, Y. / Xin, Y. / Bai, X. / Zhu, H. / Chen, H. / Wu, J. / Zheng, X. / Lin, L. / Huang, Z. / Yang, S. / Hu, F. / Liu, W.

History

Deposition	Aug 3, 2024	Deposition site: PDBJ / Processing site: PDBC
Revision 1.0	Apr 16, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9j11.cif.gz	201.3 KB	Display	PDBx/mmCIF format
PDB format	pdb9j11.ent.gz	158.4 KB	Display	PDB format
PDBx/mmJSON format	9j11.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9j11_validation.pdf.gz	465.2 KB	Display	wwPDB validaton report
Full document	9j11_full_validation.pdf.gz	471.3 KB	Display
Data in XML	9j11_validation.xml.gz	26.9 KB	Display
Data in CIF	9j11_validation.cif.gz	37.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/j1/9j11 ftp://data.pdbj.org/pub/pdb/validation_reports/j1/9j11	HTTPS FTP

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Related structure data

Related structure data	9j0qC 9j0rC 5oozS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	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 (4) #92 - Aug 2007 Anabolic Steroids similarity (1) #127 - Jul 2010 Crystallins similarity (1) #89 - May 2007 Aconitase and Iron Regulatory Protein 1 similarity (1)

Deposited unit

A: Green to red photoconvertible GFP-like protein EosFP

B: Green to red photoconvertible GFP-like protein EosFP

hetero molecules

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

1

A: Green to red photoconvertible GFP-like protein EosFP

defined by author
Evidence: gel filtration
28.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Green to red photoconvertible GFP-like protein EosFP

hetero molecules

defined by author
28.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	51.357, 82.392, 61.775
Angle α, β, γ (deg.)	90.00, 101.93, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Green to red photoconvertible GFP-like protein EosFP Mass: 28542.238 Da / Num. of mol.: 2 / Mutation: N11K,E70K,H74N,I102N,H121Y,V123T,T158E,Y189A Source method: isolated from a genetically manipulated source Details: Fusion protein: ...Details: Fusion protein: MGSSHHHHHHSQDPLEVLFQGPEFMSAIKPDMKIKLRMEGNVNGHHFVIDGDGTGKPFEGKQSMDLEVKEGGPLPFAFDILTTAFHYGNRVFAKYPDNIQDYFKQSFPKGYSWERSLTFEDGGICNARNDITMEGDTFYNKVRFYGTNFPANGPVMQKKTLKWEPSTEKMYVRDGVLTGDIEMALLLEGNAHYRCDFRTTYKAKEKGVKLPGAHFVDHCIEILSHDKDYNKVKLYEHAVAHSGLPDNARR Source: (gene. exp.) Lobophyllia hemprichii (invertebrata) / Production host: Escherichia coli (E. coli) / References: UniProt: Q5S6Z9
#2: Chemical	ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₀O₂S₂
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 431 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
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: 2.24 Å³/Da / Density % sol: 45.09 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop Details: 0.2 M Ammonium acetate, 0.1 M Sodium acetate trihydrate, pH 6.0, 30% (w/v) PEG 4000

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 4, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97853 Å / Relative weight: 1
Reflection	Resolution: 1.85→48.73 Å / Num. obs: 43073 / % possible obs: 100 % / Redundancy: 6.8 % / CC_1/2: 0.999 / Net I/σ(I): 12.8
Reflection shell	Resolution: 1.85→1.95 Å / Num. unique obs: 6286 / CC_1/2: 0.842

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Processing

Software

Name	Version	Classification
PHENIX	(1.20.1_4487: ???)	refinement
autoPROC		data reduction
autoPROC		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5OOZ

5ooz

Resolution: 1.85→28.64 Å / SU ML: 0.14 / Cross valid method: NONE / σ(F): 0.03 / Phase error: 17.84 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.184	1903	4.64 %
R_work	0.1533	-	-
obs	0.1548	41044	95.33 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.85→28.64 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3500	0	0	431	3931

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	3611
X-RAY DIFFRACTION	f_angle_d	1.462	4867
X-RAY DIFFRACTION	f_dihedral_angle_d	9.436	483
X-RAY DIFFRACTION	f_chiral_restr	0.064	493
X-RAY DIFFRACTION	f_plane_restr	0.009	631

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 (%)
1.85-1.9	0.2502	125	0.1976	2522	X-RAY DIFFRACTION	86
1.9-1.95	0.2044	123	0.1895	2622	X-RAY DIFFRACTION	89
1.95-2	0.2131	122	0.1695	2640	X-RAY DIFFRACTION	91
2-2.07	0.191	134	0.1636	2723	X-RAY DIFFRACTION	93
2.07-2.14	0.2026	133	0.161	2746	X-RAY DIFFRACTION	94
2.14-2.23	0.1998	135	0.151	2782	X-RAY DIFFRACTION	95
2.23-2.33	0.1988	136	0.1596	2801	X-RAY DIFFRACTION	96
2.33-2.45	0.2113	141	0.1623	2813	X-RAY DIFFRACTION	97
2.45-2.61	0.183	140	0.1567	2869	X-RAY DIFFRACTION	98
2.61-2.81	0.1605	141	0.1481	2877	X-RAY DIFFRACTION	98
2.81-3.09	0.1939	142	0.1476	2904	X-RAY DIFFRACTION	99
3.09-3.54	0.1923	142	0.1395	2913	X-RAY DIFFRACTION	99
3.54-4.45	0.1453	143	0.1341	2942	X-RAY DIFFRACTION	100
4.45-28.64	0.181	146	0.1635	2987	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	4.7984	-0.4566	0.2404	2.0392	0.1747	1.9479	0.0088	-0.5202	-0.178	0.2235	0.0272	-0.029	0.0189	0.0291	-0.0367	0.1598	-0.01	-0.0101	0.1443	0.0028	0.1207	0.2381	22.3059	-9.1096
2	4.1839	0.5686	0.3986	3.1946	0.48	2.8775	-0.0376	0.0035	-0.1971	0.0612	-0.0329	0.3168	0.0805	-0.3323	0.0732	0.1083	-0.0065	0.0172	0.1509	-0.0126	0.1582	-13.9532	16.8056	-17.3215
3	6.9457	3.3135	-7.4518	2.1445	-3.1831	8.2338	-0.133	-0.1445	-0.5455	-0.1262	-0.0625	-0.2436	0.2782	0.0954	0.3317	0.164	0.0078	-0.0232	0.1651	-0.0032	0.1945	1.2057	14.3736	-18.1693
4	5.2464	1.4646	-5.9665	1.6835	-1.3124	6.8477	-0.2278	-0.3816	-0.5857	0.077	0.0073	-0.0646	0.3562	0.1657	0.2066	0.1618	-0.0034	-0.0436	0.2129	-0.0031	0.1635	-0.4793	14.9455	-9.6558
5	3.2579	0.2304	-0.3178	2.0385	-0.0148	1.3608	-0.0272	0.1585	-0.008	-0.2715	0.0852	-0.2189	-0.0313	0.1375	-0.0706	0.1272	0.0177	0.0183	0.1339	-0.0148	0.1115	3.3726	22.4117	-25.6953
6	5.4197	2.1605	-0.4933	3.697	-0.3397	3.3597	-0.0362	-0.0032	-0.2144	-0.116	0.0045	-0.0161	0.1199	-0.0599	0.0277	0.1204	0.0361	-0.0064	0.114	-0.0336	0.1194	-3.6636	16.3094	-24.2501
7	5.4741	2.2503	2.0129	4.1655	1.5911	3.3385	-0.1561	-0.125	0.4109	-0.0447	0.0099	0.1196	-0.2302	0.0042	0.1783	0.11	0.0249	0.0274	0.0978	-0.0033	0.1072	-3.0876	28.8126	-16.7771
8	5.5116	-0.1424	-0.4315	0.9846	-0.0908	1.3166	-0.0408	-0.3441	-0.0004	0.1932	0.0528	0.0296	0.0024	-0.0661	-0.0137	0.2144	0.0076	0.0169	0.1436	0.007	0.1355	-11.3707	46.7563	-6.9948
9	6.4918	-1.6797	-3.4838	3.6814	0.5127	6.8823	-0.1799	0.096	-0.0676	-0.0897	-0.024	-0.286	0.1226	0.2527	0.1801	0.1754	-0.0062	-0.0311	0.1658	0.0055	0.1663	4.3614	52.626	-18.3186
10	4.3243	0.2371	1.5183	1.0568	0.0281	2.6723	-0.0783	-0.2164	0.1362	0.0867	0.0974	0.1013	-0.1492	-0.2567	0.0113	0.1536	0.0182	0.0231	0.1177	0.0028	0.1158	-13.7112	53.6013	-12.1875
11	5.5051	4.8185	-0.8856	6.5734	0.0892	1.8478	-0.0642	0.1456	0.0682	-0.3113	0.0992	0.0708	-0.0076	-0.0447	-0.0482	0.1752	0.0131	-0.0182	0.1512	0.0192	0.1068	-10.5842	51.1459	-24.1892
12	4.9729	1.0495	-0.1649	1.5897	-0.4725	3.2402	0.072	-0.0506	0.1313	0.0174	-0.0408	0.0448	-0.0831	-0.0766	-0.0034	0.1673	0.0382	0.0042	0.0844	0.0181	0.1092	-8.9849	55.2474	-20.5304
13	5.5835	2.1068	-2.3633	3.7969	-1.3553	2.9206	-0.2477	-0.1386	-0.4463	-0.0906	-0.0318	-0.0871	0.2887	0.0357	0.2942	0.1492	0.0102	-0.0011	0.105	-0.0166	0.1194	-9.0223	41.4475	-15.2804

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 60 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 61 through 86 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 87 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 163 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 164 through 189 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 190 through 219 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 2 through 65 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 66 through 79 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 80 through 135 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 136 through 163 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 164 through 189 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 190 through 219 )

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