PDB-9j0r: Structure of pcStar in the green fluorescent state

ID or keywords:

Entry

Database: PDB / ID: 9j0r

Title

Structure of pcStar in the green fluorescent state

Components

Green to red photoconvertible GFP-like protein EosFP

Keywords

FLUORESCENT PROTEIN / Green-to-red / photoconvertible

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: 1.66 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 2, 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	9j0r.cif.gz	200.1 KB	Display	PDBx/mmCIF format
PDB format	pdb9j0r.ent.gz	159 KB	Display	PDB format
PDBx/mmJSON format	9j0r.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9j0r_validation.pdf.gz	457.6 KB	Display	wwPDB validaton report
Full document	9j0r_full_validation.pdf.gz	463.6 KB	Display
Data in XML	9j0r_validation.xml.gz	27.6 KB	Display
Data in CIF	9j0r_validation.cif.gz	37.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/j0/9j0r ftp://data.pdbj.org/pub/pdb/validation_reports/j0/9j0r	HTTPS FTP

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Related structure data

Related structure data	9j0qC 9j11C 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

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

1

A: Green to red photoconvertible GFP-like protein EosFP

hetero molecules

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

2

B: Green to red photoconvertible GFP-like protein EosFP

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

Unit cell

Length a, b, c (Å)	50.846, 76.768, 124.193
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Green to red photoconvertible GFP-like protein EosFP Mass: 26168.688 Da / Num. of mol.: 2 Mutation: N11K,D28E,E70K,H74N,L93M,I102N,H121Y,V123T,T158E,N166G,Y189A Source method: isolated from a genetically manipulated source Details: Fusion protein: ...Details: Fusion protein: MGSSHHHHHHSQDPLEVLFQGPEFMSAIKPDMKIKLRMEGNVNGHHFVIDGEGTGKPFEGKQSMDLEVKEGGPLPFAFDILTTAFHYGNRVFAKYPDNIQDYFKQSFPKGYSWERSMTFEDGGICNARNDITMEGDTFYNKVRFYGTNFPANGPVMQKKTLKWEPSTEKMYVRDGVLTGDIEMALLLEGGAHYRCDFRTTYKAKEKGVKLPGAHFVDHCIEILSHDKDYNKVKLYEHAVAHSGLPDNARR PreScission digestion 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.: 466 / 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: 2.45 Å³/Da / Density % sol: 49.87 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop Details: 0.2 M Ammonium acetate, 0.1 M Sodium acetate trihydrate, pH 4.78 27% (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: BL19U1 / Wavelength: 0.97851 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 7, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97851 Å / Relative weight: 1
Reflection	Resolution: 1.66→65.3 Å / Num. obs: 58118 / % possible obs: 99.6 % / Redundancy: 5.3 % / B_iso Wilson estimate: 20.33 Å² / CC_1/2: 0.998 / Net I/σ(I): 14.1
Reflection shell	Resolution: 1.66→1.75 Å / Num. unique obs: 8391 / CC_1/2: 0.998

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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: 1.66→28.15 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.64 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1896	1999	3.44 %	RANDOM
R_work	0.1608	-	-	-
obs	0.1618	58037	99.46 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.66→28.15 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3482	0	0	466	3948

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	3585
X-RAY DIFFRACTION	f_angle_d	1.478	4825
X-RAY DIFFRACTION	f_dihedral_angle_d	9.54	477
X-RAY DIFFRACTION	f_chiral_restr	0.061	485
X-RAY DIFFRACTION	f_plane_restr	0.008	625

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 (%)
1.66-1.7	0.2602	141	0.2307	3971	X-RAY DIFFRACTION	99
1.7-1.75	0.2529	141	0.2163	3956	X-RAY DIFFRACTION	100
1.75-1.8	0.2593	140	0.2124	3937	X-RAY DIFFRACTION	100
1.8-1.86	0.2613	141	0.2099	3947	X-RAY DIFFRACTION	100
1.86-1.92	0.2183	142	0.1853	3983	X-RAY DIFFRACTION	100
1.92-2	0.1905	143	0.1701	3986	X-RAY DIFFRACTION	100
2-2.09	0.1935	142	0.1665	3996	X-RAY DIFFRACTION	100
2.09-2.2	0.1853	143	0.1602	3992	X-RAY DIFFRACTION	100
2.2-2.34	0.1838	142	0.1584	3996	X-RAY DIFFRACTION	100
2.34-2.52	0.1892	141	0.1652	3967	X-RAY DIFFRACTION	99
2.52-2.77	0.1805	144	0.1617	4018	X-RAY DIFFRACTION	99
2.77-3.17	0.1735	144	0.1584	4048	X-RAY DIFFRACTION	99
3.17-3.99	0.1899	145	0.1406	4038	X-RAY DIFFRACTION	99
4-28.15	0.1631	150	0.144	4203	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	3.7797	0.6027	-0.2897	2.6284	-0.0515	2.1357	-0.5381	0.6832	-0.288	-0.7793	0.3782	-0.1225	0.306	-0.1412	0.0413	0.3581	-0.0554	-0.0081	0.194	-0.0303	0.1206	8.2968	27.2343	66.8822
2	1.9075	0.5931	-0.625	3.4701	-1.003	2.1408	-0.1637	0.1169	0.0093	-0.3823	-0.0389	-0.3533	0.2627	0.1471	0.0819	0.1859	-0.0028	0.0316	0.1274	0.0025	0.1201	13.1614	27.1222	74.1248
3	8.3755	-2.0994	-4.6628	4.4656	0.7409	4.5764	-0.1011	0.1086	0.0612	0.0592	0.1565	0.0734	0.3678	-0.2818	0.0619	0.1423	-0.0307	-0.0157	0.1188	0.0135	0.0728	2.6099	21.9226	81.4469
4	7.8757	-0.7793	-4.5177	2.5381	0.3971	4.4638	-0.2967	0.3056	-0.4134	-0.5315	0.1366	-0.0808	0.3825	-0.0424	0.2266	0.3121	-0.0468	0.0136	0.1824	-0.0419	0.1296	8.0309	20.7369	70.0369
5	4.4603	0.519	0.1514	5.2925	0.2828	2.1972	0.0356	0.0522	0.3951	0.017	0.1945	1.5787	-0.0433	-0.6717	-0.179	0.1465	0.0007	-0.0084	0.3143	0.0441	0.3924	-10.4819	32.5659	80.4713
6	3.5345	-2.7107	0.3384	5.4867	-0.3122	0.8406	0.0261	-0.1664	-0.0996	0.3539	0.0252	0.1919	0.0457	-0.032	-0.0623	0.1781	-0.0222	0.0023	0.1632	0.0116	0.1321	8.3783	26.0935	86.8265
7	2.1508	0.4985	0.0108	2.7086	-1.0159	1.9412	-0.0308	0.0714	0.0354	-0.0597	0.0186	0.1369	0.0765	-0.027	0.0307	0.1427	-0.0098	-0.0103	0.1274	-0.0044	0.0657	8.6989	27.3417	80.4311
8	5.5135	-1.1036	2.3474	4.1624	-1.7672	3.7631	-0.1094	-0.1437	0.165	-0.0405	0.0437	-0.2451	0.0522	-0.0146	0.0127	0.1434	-0.0327	0.0004	0.1118	-0.0025	0.1154	14.5691	33.6188	78.3061
9	5.8127	0.6022	0.91	1.911	-0.3063	2.8952	-0.2653	0.4	0.2695	-0.2383	0.1546	-0.001	-0.1643	0.1039	0.0931	0.1848	-0.0076	0.016	0.1289	0.0075	0.1397	19.189	56.7031	70.1004
10	2.386	-0.0358	-0.2398	1.6688	0.0737	2.0263	-0.0354	0.1319	0.0267	-0.1892	-0.0038	-0.0791	0.0415	0.0627	0.0494	0.1601	-0.0188	0.0274	0.1315	-0.0094	0.1288	20.6874	51.7127	74.0341
11	2.1595	0.5161	-0.7493	4.3961	0.659	4.2132	0.1224	-0.0662	-0.0498	0.0642	-0.2277	0.5352	-0.0205	-0.4619	0.0748	0.129	0.0075	0.0085	0.2076	-0.0077	0.2365	3.067	58.2876	82.844
12	5.4684	-1.5853	2.9143	2.3662	-1.1531	3.5028	-0.102	0.0231	0.2244	0.077	0.0384	0.0541	-0.2916	0.0099	0.1104	0.1272	-0.0075	0.0157	0.1293	-0.0248	0.1349	17.0076	61.854	82.0004
13	8.5623	-0.8782	5.0179	2.5354	-1.2048	5.2765	-0.2164	0.2607	0.4891	-0.1648	0.0325	-0.1148	-0.3058	0.1453	0.2776	0.1779	-0.0134	0.028	0.1446	0.0047	0.1418	19.3262	62.4397	74.0602
14	5.1721	0.7724	0.0238	3.4834	-0.9609	2.8981	-0.0661	0.0246	-0.2396	-0.0671	-0.1082	-1.2981	0.2141	0.536	0.0514	0.109	0.0251	0.0015	0.276	-0.0121	0.3382	36.7013	48.7276	84.1321
15	3.583	-2.7447	-0.3606	3.9614	-0.0152	1.3671	-0.0274	-0.3256	0.2502	0.4114	0.1307	-0.1884	-0.1122	0.0304	-0.132	0.1566	-0.0327	0.0148	0.168	-0.0447	0.1481	17.3348	54.4675	89.8033
16	2.6784	-0.7652	0.2598	2.1235	-0.1647	2.1492	0.0355	-0.0245	0.2269	0.1459	-0.0026	-0.014	-0.1835	-0.0578	-0.0076	0.1658	-0.0143	0.0267	0.1379	-0.0331	0.1451	16.0093	59.7695	87.0963
17	2.591	-0.7717	-0.752	2.7405	0.3741	1.4732	-0.1359	-0.0002	-0.1274	0.0144	0.0271	0.0419	0.1832	0.0413	0.1288	0.1424	-0.0178	0.0135	0.1311	-0.0134	0.1252	16.3163	47.2528	78.7977

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 3 through 32 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 33 through 86 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 87 through 99 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 100 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 163 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 164 through 206 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 207 through 219 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 3 through 32 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 33 through 65 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 66 through 79 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 80 through 99 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 100 through 123 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 124 through 135 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 136 through 163 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 164 through 189 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 190 through 219 )

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