PDB-6ofn: Crystal structure of green fluorescent protein (GFP); S65T, T203(...

ID or keywords:

Entry

Database: PDB / ID: 6ofn

Title

Crystal structure of green fluorescent protein (GFP); S65T, T203(3-OMeY); ih circular permutant (50-51)

Components

Green fluorescent protein (GFP); S65T, T203(3-OMeY); ih circular permutant (50-51)

Keywords

FLUORESCENT PROTEIN / GFP

Function / homology

Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / generation of precursor metabolites and energy / Green fluorescent protein

Function and homology information

Biological species

Aequorea victoria (jellyfish)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.649 Å

Authors

Lin, C.-Y. / Romei, M.G. / Mathews, I.I. / Boxer, S.G.

Funding support

United States, 1items

Citation

Journal: J.Am.Chem.Soc. / Year: 2019
Title: Unified Model for Photophysical and Electro-Optical Properties of Green Fluorescent Proteins.
Authors: Lin, C.Y. / Romei, M.G. / Oltrogge, L.M. / Mathews, I.I. / Boxer, S.G.

History

Deposition	Mar 31, 2019	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 10, 2019	Provider: repository / Type: Initial release
Revision 1.1	Oct 2, 2019	Group: Data collection / Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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.identifier_ORCID / _citation_author.name
Revision 1.2	Jan 1, 2020	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3	Oct 11, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4	Nov 15, 2023	Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	6ofn.cif.gz	208.4 KB	Display	PDBx/mmCIF format
PDB format	pdb6ofn.ent.gz	165.9 KB	Display	PDB format
PDBx/mmJSON format	6ofn.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/of/6ofn ftp://data.pdbj.org/pub/pdb/validation_reports/of/6ofn	HTTPS FTP

-
Related structure data

Related structure data	6ofkC 6oflC 6ofmC 6ofoC 4zf3S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	7a89-2 7a8h-1 7a80-3 3sve-d 7a7n-d 1emb-d 5t3i-d 3ssy-d 1qxt-d 2ye1-d 3w1c-d 4w74-3 6qq9-d 2q57-d 1qyf-d 6og8-2 1q4e-d 4zf4-1 4w76-1 6aa2-1 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

Related structure data

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

-
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 (5)

Deposited unit

A: Green fluorescent protein (GFP); S65T, T203(3-OMeY); ih circular permutant (50-51)

B: Green fluorescent protein (GFP); S65T, T203(3-OMeY); ih circular permutant (50-51)

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

1

A: Green fluorescent protein (GFP); S65T, T203(3-OMeY); ih circular permutant (50-51)

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

2

B: Green fluorescent protein (GFP); S65T, T203(3-OMeY); ih circular permutant (50-51)

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

Unit cell

Length a, b, c (Å)	48.190, 67.763, 58.849
Angle α, β, γ (deg.)	90.00, 101.51, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Green fluorescent protein (GFP); S65T, T203(3-OMeY); ih circular permutant (50-51) Mass: 28175.430 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aequorea victoria (jellyfish) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P42212*PLUS
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 290 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 1.67 Å³/Da / Density % sol: 26.38 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, hanging drop / Details: 0.15 M ammonium acetate, 34% PEG 3350

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 4, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 1.649→38.742 Å / Num. obs: 43982 / % possible obs: 98.1 % / Redundancy: 13.6 % / B_iso Wilson estimate: 21.9 Å² / CC_1/2: 1 / R_rim(I) all: 0.075 / Net I/σ(I): 21.3
Reflection shell	Resolution: 1.65→1.71 Å / Redundancy: 12.9 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4295 / CC_1/2: 0.671 / R_rim(I) all: 1.48 / % possible all: 96.3

-
Processing

Software

Name	Version	Classification
PHENIX	(1.13rc2_2986: ???)	refinement
XDS		data reduction
XDS		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4zf3

4zf3

Resolution: 1.649→38.742 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.92

	R_factor	Num. reflection	% reflection
R_free	0.1909	2199	5 %
R_work	0.1623	-	-
obs	0.1637	43957	98.06 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 1.649→38.742 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3677	0	0	290	3967

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	3904
X-RAY DIFFRACTION	f_angle_d	0.781	5314
X-RAY DIFFRACTION	f_dihedral_angle_d	3.088	3166
X-RAY DIFFRACTION	f_chiral_restr	0.053	587
X-RAY DIFFRACTION	f_plane_restr	0.004	696

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 (%)
1.6487-1.6845	0.2702	133	0.2704	2531	X-RAY DIFFRACTION	95
1.6845-1.7237	0.2808	136	0.257	2577	X-RAY DIFFRACTION	97
1.7237-1.7668	0.3134	136	0.2423	2573	X-RAY DIFFRACTION	98
1.7668-1.8146	0.2764	137	0.2208	2616	X-RAY DIFFRACTION	99
1.8146-1.868	0.2362	138	0.2023	2608	X-RAY DIFFRACTION	99
1.868-1.9283	0.2026	138	0.1899	2624	X-RAY DIFFRACTION	99
1.9283-1.9972	0.2267	139	0.1813	2633	X-RAY DIFFRACTION	99
1.9972-2.0771	0.2285	133	0.1721	2534	X-RAY DIFFRACTION	97
2.0771-2.1717	0.2148	138	0.1666	2623	X-RAY DIFFRACTION	99
2.1717-2.2861	0.1711	138	0.165	2628	X-RAY DIFFRACTION	99
2.2861-2.4293	0.1903	138	0.164	2635	X-RAY DIFFRACTION	99
2.4293-2.6169	0.1956	139	0.1697	2617	X-RAY DIFFRACTION	98
2.6169-2.8801	0.2007	136	0.1736	2604	X-RAY DIFFRACTION	99
2.8801-3.2967	0.1809	139	0.1556	2640	X-RAY DIFFRACTION	99
3.2967-4.1528	0.1609	139	0.1322	2616	X-RAY DIFFRACTION	97
4.1528-38.7527	0.1589	142	0.1343	2699	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	0.1692	0.7267	0.4802	5.209	-0.5046	3.9905	0.114	-0.231	-0.0515	0.122	-0.213	-0.4753	-0.0496	0.3795	0.0699	0.1774	0.0034	-0.0243	0.2173	0.0268	0.1862	15.3071	11.0102	0.1819
2	4.1029	-1.6575	-0.3078	2.5462	-0.7899	3.4586	0.0712	-0.5936	-0.0822	0.5125	0.0774	0.6595	-0.2349	-0.5466	-0.0946	0.2509	-0.0203	0.0882	0.3456	-0.059	0.3792	-8.2358	9.0362	8.2295
3	2.1468	1.5703	-0.6424	3.5115	-0.4444	1.315	0.0007	0.0561	-0.012	-0.1096	-0.0399	0.0443	0.095	-0.0608	0.0686	0.2066	0.0059	-0.0125	0.1777	-0.0042	0.124	5.0688	6.9193	-5.2137
4	1.14	-0.0273	0.281	1.7557	1.0397	2.7017	0.1447	-0.0637	0.0427	0.1488	-0.0668	-0.2935	-0.139	0.5032	-0.0839	0.2037	-0.0264	-0.0039	0.2318	0.0241	0.2403	18.4951	20.4339	-0.4487
5	4.1721	2.0057	0.731	3.621	0.2657	1.7035	-0.071	0.1609	0.2098	-0.0789	0.0424	0.3499	-0.039	-0.0434	0.0269	0.2045	0.0159	-0.0168	0.1849	-0.026	0.2222	2.2361	18.8363	-2.2484
6	9.3535	2.9727	3.368	2.1357	1.6392	2.0842	-0.0416	-0.0193	0.5053	-0.0802	-0.1148	0.4508	-0.0086	-0.0704	0.1554	0.1868	0.0115	-0.0266	0.1937	-0.003	0.1663	3.7494	16.6843	-5.8183
7	0.9903	0.0972	-0.2542	2.783	0.013	1.6724	0.0189	-0.0362	0.202	0.2188	-0.1252	0.5238	-0.0509	-0.1491	0.0939	0.2139	-0.0259	0.0598	0.1998	-0.0249	0.2213	-2.9643	11.2688	3.1627
8	6.5242	-1.2567	-1.8476	2.9759	0.7351	3.8796	-0.1403	-0.2819	-0.2205	0.8367	0.0311	-0.6384	0.5071	0.723	0.0768	0.3772	-0.0107	-0.1637	0.3747	0.0489	0.3033	19.6229	5.7777	9.8654
9	0.2967	1.1438	0.1831	5.9275	2.3488	1.6186	0.3135	-0.5024	0.2956	0.9308	-0.5477	1.0005	0.0911	-0.2127	0.1725	0.3278	-0.0799	0.1146	0.3144	-0.0763	0.3461	-7.8386	4.1139	8.398
10	3.2591	1.6423	-2.6834	4.0364	-1.9117	5.6813	-0.1075	-0.0123	-0.436	-0.0801	-0.1928	-0.5043	0.4519	0.1582	0.3672	0.1993	0.0269	-0.0235	0.1603	0.0423	0.1695	13.7046	2.5738	-0.6026
11	6.4726	-0.2784	-0.7613	3.2508	0.4937	2.1583	0.009	-0.6802	-0.223	0.7884	-0.2221	-0.2288	0.3091	0.3294	0.244	0.3037	-0.0519	-0.0625	0.2283	0.0476	0.1666	9.8959	3.9383	9.0978
12	4.039	-2.4084	1.5492	2.9546	-0.4436	2.9855	-0.1856	-0.1582	0.0093	-0.0734	0.1976	0.14	-0.0848	-0.2699	0.0053	0.2463	-0.022	0.0003	0.1781	0.027	0.1609	5.1143	22.2979	27.427
13	3.0739	-0.2938	0.061	1.9275	-0.9112	1.8823	-0.2221	-0.1445	0.1163	0.2496	0.0099	-0.3327	-0.2352	0.1911	0.1997	0.2644	-0.0273	-0.0236	0.1533	0.0183	0.1713	18.4898	24.0652	31.4654
14	2.3968	0.3319	0.991	3.3626	-0.3646	3.1053	0.0064	0.07	0.1912	0.1027	0.127	0.2299	-0.0833	-0.4546	-0.1229	0.2441	-0.0198	-0.0009	0.2292	0.0695	0.2185	0.6178	28.3651	21.04
15	7.3224	-0.363	3.884	1.7922	-0.5899	3.2968	-0.0774	-0.2173	0.2317	0.1346	-0.0488	-0.3562	-0.2162	-0.0048	0.0918	0.2779	-0.046	-0.0093	0.2151	0.0177	0.2481	16.9803	31.9028	23.1644
16	3.7464	-0.7659	0.4792	1.1364	-0.2553	2.0788	-0.3181	-0.2361	0.5535	0.2343	0.0494	-0.3924	-0.2879	0.3436	0.2467	0.3411	-0.0647	-0.0862	0.2421	0.0022	0.3097	21.8595	30.2139	29.5275
17	2.6029	-0.8107	0.7385	1.6224	0.1601	2.3378	-0.3055	0.2834	-0.3498	-0.1644	0.1616	0.0144	0.3593	-0.0796	0.0762	0.3091	-0.0598	0.0292	0.1517	0.0072	0.1707	9.9221	15.6308	21.9926
18	4.4693	-1.7303	-0.8783	1.8898	1.9153	3.7791	-0.4002	0.9644	-0.5965	-0.3547	0.5228	-0.361	0.7415	0.5475	0.051	0.3221	-0.146	0.0907	0.8773	0.073	0.6035	38.9009	18.3305	21.1158
19	2.3918	-0.0513	0.1172	2.9921	-0.9147	2.06	-0.2044	-0.1062	-0.3819	0.1822	0.0992	-0.0107	0.0961	-0.0625	0.1104	0.2724	0.0028	0.0248	0.1763	0.035	0.184	11.8099	15.4622	32.0269

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	( CHAIN A AND RESID 2:18 )	A	2 - 18
2	X-RAY DIFFRACTION	2	( CHAIN A AND RESID 19:31 )	A	19 - 31
3	X-RAY DIFFRACTION	3	( CHAIN A AND RESID 32:78 )	A	32 - 78
4	X-RAY DIFFRACTION	4	( CHAIN A AND RESID 79:99 )	A	79 - 99
5	X-RAY DIFFRACTION	5	( CHAIN A AND RESID 100:125 )	A	100 - 125
6	X-RAY DIFFRACTION	6	( CHAIN A AND RESID 126:137 )	A	126 - 137
7	X-RAY DIFFRACTION	7	( CHAIN A AND RESID 138:158 )	A	138 - 158
8	X-RAY DIFFRACTION	8	( CHAIN A AND RESID 159:173 )	A	159 - 173
9	X-RAY DIFFRACTION	9	( CHAIN A AND RESID 174:203 )	A	174 - 203
10	X-RAY DIFFRACTION	10	( CHAIN A AND RESID 204:229 )	A	204 - 229
11	X-RAY DIFFRACTION	11	( CHAIN A AND RESID 230:242 )	A	230 - 242
12	X-RAY DIFFRACTION	12	( CHAIN B AND RESID 2:18 )	B	2 - 18
13	X-RAY DIFFRACTION	13	( CHAIN B AND RESID 19:78 )	B	19 - 78
14	X-RAY DIFFRACTION	14	( CHAIN B AND RESID 79:99 )	B	79 - 99
15	X-RAY DIFFRACTION	15	( CHAIN B AND RESID 100:125 )	B	100 - 125
16	X-RAY DIFFRACTION	16	( CHAIN B AND RESID 126:148 )	B	126 - 148
17	X-RAY DIFFRACTION	17	( CHAIN B AND RESID 149:177 )	B	149 - 177
18	X-RAY DIFFRACTION	18	( CHAIN B AND RESID 178:196 )	B	178 - 196
19	X-RAY DIFFRACTION	19	( CHAIN B AND RESID 197:243 )	B	197 - 243

-
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