PDB-6ogb: Crystal structure of Green Fluorescent Protein (GFP); S65T, Y66(3...

ID or keywords:

Entry

Database: PDB / ID: 6ogb

Title

Crystal structure of Green Fluorescent Protein (GFP); S65T, Y66(3-I1Y), H148D; circular permutant (50-51)

Components

Crystal structure of Green Fluorescent Protein (GFP); S65T, Y66(3-I1Y), H148D; 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 / ACETATE ION / Green fluorescent protein

Function and homology information

Biological species

Aequorea victoria (jellyfish)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.65 Å

Authors

Lin, C.-Y. / Boxer, S.G.

Funding support

United States, 1items

Citation

Journal: J.Phys.Chem.B / Year: 2020
Title: Unusual Spectroscopic and Electric Field Sensitivity of Chromophores with Short Hydrogen Bonds: GFP and PYP as Model Systems.
Authors: Lin, C.Y. / Boxer, S.G.

History

Deposition	Apr 2, 2019	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 8, 2020	Provider: repository / Type: Initial release
Revision 1.1	Oct 28, 2020	Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Nov 4, 2020	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
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 / Derived calculations / Category: chem_comp_atom / chem_comp_bond / struct_conn Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 ..._chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6ogb.cif.gz	207.5 KB	Display	PDBx/mmCIF format
PDB format	pdb6ogb.ent.gz	165.1 KB	Display	PDB format
PDBx/mmJSON format	6ogb.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6ogb_validation.pdf.gz	466.1 KB	Display	wwPDB validaton report
Full document	6ogb_full_validation.pdf.gz	471.8 KB	Display
Data in XML	6ogb_validation.xml.gz	23.8 KB	Display
Data in CIF	6ogb_validation.cif.gz	33.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/og/6ogb ftp://data.pdbj.org/pub/pdb/validation_reports/og/6ogb	HTTPS FTP

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Related structure data

Related structure data	6og8C 6og9C 6ogaC 6ogcC 6un5C 6un6C 6un7C 4zf3S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	7a89-1 7a7n-d 5wj4-1 6og8-2 6oga-1 5dtz-1 6ofn-1 6gqh-d 2duh-d 1qxt-d 5jzl-2 7a89-2 3w1c-d 3w1d-d 1yhg-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

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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 (5)

Deposited unit

A: Crystal structure of Green Fluorescent Protein (GFP); S65T, Y66(3-I1Y), H148D; circular permutant (50-51)

B: Crystal structure of Green Fluorescent Protein (GFP); S65T, Y66(3-I1Y), H148D; circular permutant (50-51)

hetero molecules

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

1

A: Crystal structure of Green Fluorescent Protein (GFP); S65T, Y66(3-I1Y), H148D; circular permutant (50-51)

hetero molecules

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

2

B: Crystal structure of Green Fluorescent Protein (GFP); S65T, Y66(3-I1Y), H148D; circular permutant (50-51)

hetero molecules

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

Unit cell

Length a, b, c (Å)	51.810, 68.690, 61.640
Angle α, β, γ (deg.)	90.00, 99.762, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Crystal structure of Green Fluorescent Protein (GFP); S65T, Y66(3-I1Y), H148D; circular permutant (50-51) Mass: 28186.170 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: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₂H₃O₂
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 339 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 1.92 Å³/Da / Density % sol: 35.85 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 50 mM sodium acetate, pH 5.0, 100 mM NaCl, 7-8% PEG 3350

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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: Nov 2, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 1.65→36.182 Å / Num. obs: 50444 / % possible obs: 98.3 % / Redundancy: 5.7 % / B_iso Wilson estimate: 21.23 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.07952 / R_pim(I) all: 0.0359 / R_rim(I) all: 0.08748 / Net I/σ(I): 13.08
Reflection shell	Resolution: 1.65→1.709 Å / Redundancy: 5.5 % / R_merge(I) obs: 0.9559 / Mean I/σ(I) obs: 1.61 / Num. unique obs: 4904 / CC_1/2: 0.656 / R_pim(I) all: 0.4425 / R_rim(I) all: 1.057 / % possible all: 95.58

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Processing

Software

Name	Version	Classification
PHENIX	(1.12_2829: ???)	refinement
XDS		data reduction
XDS		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4zf3

4zf3

Resolution: 1.65→36.182 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.91

	R_factor	Num. reflection	% reflection
R_free	0.1776	2523	5 %
R_work	0.1559	-	-
obs	0.157	50438	98.3 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.65→36.182 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3590	0	44	339	3973

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	3884
X-RAY DIFFRACTION	f_angle_d	0.87	5262
X-RAY DIFFRACTION	f_dihedral_angle_d	15.121	2287
X-RAY DIFFRACTION	f_chiral_restr	0.061	578
X-RAY DIFFRACTION	f_plane_restr	0.005	689

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 (%)
1.65-1.6817	0.3446	138	0.2842	2619	X-RAY DIFFRACTION	97
1.6817-1.716	0.2788	135	0.2744	2560	X-RAY DIFFRACTION	95
1.716-1.7534	0.2871	139	0.2355	2642	X-RAY DIFFRACTION	99
1.7534-1.7941	0.2772	143	0.2189	2714	X-RAY DIFFRACTION	99
1.7941-1.839	0.2248	139	0.199	2653	X-RAY DIFFRACTION	99
1.839-1.8887	0.2045	141	0.1816	2660	X-RAY DIFFRACTION	99
1.8887-1.9443	0.2057	139	0.1673	2660	X-RAY DIFFRACTION	99
1.9443-2.007	0.1929	139	0.1597	2641	X-RAY DIFFRACTION	97
2.007-2.0788	0.1719	136	0.1572	2581	X-RAY DIFFRACTION	96
2.0788-2.162	0.1751	142	0.1494	2692	X-RAY DIFFRACTION	100
2.162-2.2604	0.1559	142	0.1478	2697	X-RAY DIFFRACTION	100
2.2604-2.3795	0.1715	142	0.152	2690	X-RAY DIFFRACTION	99
2.3795-2.5286	0.1827	140	0.1532	2670	X-RAY DIFFRACTION	99
2.5286-2.7238	0.1753	139	0.1552	2644	X-RAY DIFFRACTION	97
2.7238-2.9977	0.1766	142	0.1503	2684	X-RAY DIFFRACTION	100
2.9977-3.4312	0.162	142	0.1368	2712	X-RAY DIFFRACTION	99
3.4312-4.3218	0.1501	141	0.1322	2670	X-RAY DIFFRACTION	98
4.3218-36.1903	0.159	144	0.1496	2726	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	2.4232	1.2223	-0.4647	3.332	-0.1525	4.0585	-0.0906	-0.1646	0.0596	0.0594	-0.0255	-0.2423	-0.1646	0.1522	0.1199	0.2195	0.0121	-0.0186	0.1684	0.013	0.1916	14.3347	11.7776	0.6802
2	9.6404	-2.4032	-2.389	5.9152	1.5555	6.6262	-0.0059	-0.3309	0.149	0.3474	0.0541	0.4894	0.0176	-0.3229	-0.0249	0.2143	-0.011	0.042	0.1457	-0.0042	0.2131	-8.5635	9.8404	7.9251
3	2.9376	1.6287	-1.0666	2.4671	-0.9909	0.7883	-0.0292	0.1569	0.1123	-0.1839	0.063	0.0491	0.0234	-0.0185	-0.0554	0.1981	0.0081	0	0.1482	-0.0026	0.1385	2.1281	11.2444	-4.7325
4	4.0701	3.2565	-1.6521	5.8505	-2.0584	2.861	-0.2232	0.259	-0.1551	-0.4481	0.0825	-0.1753	0.2956	-0.0568	0.1197	0.1741	0.0163	0.0089	0.1213	-0.0211	0.1227	7.607	4.6214	-6.1617
5	2.7835	0.137	1.3427	1.7506	-0.2896	3.2092	0.073	0.2402	0.2104	0.0264	-0.0348	-0.4658	-0.0876	0.4912	-0.0264	0.1758	0.0065	0.0218	0.1609	-0.0016	0.3141	18.9008	20.6951	-0.379
6	3.2005	3.0445	1.5727	4.0368	1.3602	1.1303	-0.2989	0.4277	0.0411	-0.2066	0.2137	-0.0493	-0.2565	0.0851	0.1025	0.2401	-0.0023	-0.0135	0.1693	0.0073	0.1856	1.9122	19.5979	-1.7043
7	2.7233	0.3414	-0.1967	0.3005	0.1501	0.8257	-0.1102	0.2731	0.0821	-0.0891	0.0713	0.1172	0.0312	-0.0814	0.0574	0.1999	0.0039	-0.016	0.1653	0.0137	0.1529	-2.8528	13.4377	-5.298
8	4.8331	-0.4529	-0.0133	1.2801	0.2383	0.8896	-0.1394	-0.2825	-0.0049	0.1576	0.107	-0.145	0.0517	0.104	0.0312	0.2051	0.0228	-0.0051	0.1522	-0.0009	0.1417	10.9238	10.8285	9.7496
9	4.1384	-0.5375	0.6116	3.5548	0.6433	1.8277	0.179	-0.2458	-0.359	0.2457	-0.0378	0.6101	-0.1729	-0.3267	-0.0591	0.2257	-0.0052	0.0859	0.2008	0.002	0.219	-9.8195	2.3213	8.0028
10	5.9179	4.7288	-5.993	5.4548	-5.8139	8.1239	-0.1727	0.1263	-0.0652	-0.3694	0.075	-0.1666	0.4217	0.0235	0.1909	0.201	0.0196	0.0245	0.1358	-0.002	0.1782	13.3797	4.1404	-3.7847
11	8.5409	1.643	-6.0781	3.0264	-2.0669	5.0345	-0.435	-0.0069	-0.6044	-0.1134	-0.1144	-0.332	0.4579	0.1742	0.5616	0.2036	0.0009	-0.0138	0.1914	-0.0292	0.1455	14.9996	3.1643	0.3411
12	8.3614	-2.1019	-3.2038	3.3908	1.2648	2.9364	0.0958	0.0525	0.1086	0.0148	0.0088	-0.2266	0.0684	0.0901	-0.0672	0.1947	0.0164	-0.0204	0.1429	-0.0011	0.1421	11.6404	4.1733	7.3802
13	4.6691	-2.2196	-0.24	4.6091	0.2935	4.6037	-0.1889	0.0972	-0.0986	-0.1288	0.1634	0.182	0.0742	-0.0944	0.0298	0.212	-0.0213	-0.0126	0.175	0.0081	0.1572	4.7273	21.975	27.8272
14	6.3073	-0.8121	-1.6087	1.9482	0.7196	2.2292	-0.0769	-0.3647	-0.5752	-0.5095	-0.1608	-0.6367	0.3032	0.8282	0.0533	0.2717	0.1273	0.1315	0.4238	0.0726	0.3574	28.0913	17.3486	24.1829
15	3.0895	-0.8626	-0.4464	2.2496	-0.6512	2.646	-0.1364	-0.5514	0.0169	0.3163	0.0575	-0.134	-0.0745	0.4644	0.0649	0.1594	0.0185	-0.0133	0.2864	-0.001	0.1059	13.9999	23.8054	35.2289
16	3.8417	-1.3968	-1.0753	3.6117	1.7074	4.9218	0.1826	0.1362	0.2465	-0.1418	-0.1194	0.1042	-0.2196	-0.5147	-0.0843	0.1781	0.0029	0.0008	0.1988	0.0442	0.2103	0.0139	28.5239	22.1191
17	2.4065	-1.258	0.4619	1.6677	-0.9703	3.051	0.0509	-0.4914	0.3289	0.1024	-0.0429	-0.2701	-0.2159	0.3	0.1094	0.1854	-0.056	0.0023	0.2234	-0.0331	0.1722	15.6679	30.4526	23.7003
18	1.4772	0.052	-0.9319	1.0274	-0.367	2.6457	-0.0647	-0.2738	-0.0639	0.0322	0.0354	-0.1282	0.0977	0.3766	0.0122	0.1404	0.0168	-0.0115	0.1969	0.0036	0.1224	14.4489	22.1667	26.9091
19	1.3173	0.6004	-0.465	1.6875	-0.359	2.3663	-0.1988	-0.3048	-0.3497	-0.0553	-0.0081	-0.2909	0.3099	0.4661	0.0706	0.2168	0.0772	0.0478	0.2541	0.0685	0.2243	17.6333	14.7161	29.1074
20	4.5923	-0.8894	-2.4499	4.1729	-0.1301	4.3354	-0.3171	-0.3004	-0.5667	0.2696	0.0726	0.5526	0.3546	-0.0034	0.2244	0.1387	0.0166	-0.0177	0.2205	0.0272	0.1099	3.7888	17.5332	34.1436
21	2.3855	0.2143	-2.1839	2.222	0.0001	3.0836	-0.2745	-0.225	-0.3502	-0.2162	0.0713	0.0659	0.4572	0.0915	0.1145	0.2887	0.0465	0.0205	0.186	0.0353	0.145	9.0535	12.0126	27.9523

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 1:18 )	A	1 - 18
2	X-RAY DIFFRACTION	2	( CHAIN A AND RESID 19:31 )	A	19 - 31
3	X-RAY DIFFRACTION	3	( CHAIN A AND RESID 32:54 )	A	32 - 54
4	X-RAY DIFFRACTION	4	( CHAIN A AND RESID 55:78 )	A	55 - 78
5	X-RAY DIFFRACTION	5	( CHAIN A AND RESID 79:98 )	A	79 - 98
6	X-RAY DIFFRACTION	6	( CHAIN A AND RESID 99:125 )	A	99 - 125
7	X-RAY DIFFRACTION	7	( CHAIN A AND RESID 126:148 )	A	126 - 148
8	X-RAY DIFFRACTION	8	( CHAIN A AND RESID 149:177 )	A	149 - 177
9	X-RAY DIFFRACTION	9	( CHAIN A AND RESID 178:204 )	A	178 - 204
10	X-RAY DIFFRACTION	10	( CHAIN A AND RESID 205:217 )	A	205 - 217
11	X-RAY DIFFRACTION	11	( CHAIN A AND RESID 218:229 )	A	218 - 229
12	X-RAY DIFFRACTION	12	( CHAIN A AND RESID 230:242 )	A	230 - 242
13	X-RAY DIFFRACTION	13	( CHAIN B AND RESID 2:18 )	B	2 - 18
14	X-RAY DIFFRACTION	14	( CHAIN B AND RESID 19:31 )	B	19 - 31
15	X-RAY DIFFRACTION	15	( CHAIN B AND RESID 32:78 )	B	32 - 78
16	X-RAY DIFFRACTION	16	( CHAIN B AND RESID 79:98 )	B	79 - 98
17	X-RAY DIFFRACTION	17	( CHAIN B AND RESID 99:125 )	B	99 - 125
18	X-RAY DIFFRACTION	18	( CHAIN B AND RESID 126:166 )	B	126 - 166
19	X-RAY DIFFRACTION	19	( CHAIN B AND RESID 167:215 )	B	167 - 215
20	X-RAY DIFFRACTION	20	( CHAIN B AND RESID 216:229 )	B	216 - 229
21	X-RAY DIFFRACTION	21	( CHAIN B AND RESID 230:243 )	B	230 - 243

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Yorodumi