PDB-6un7: Crystal structure of green fluorescent protein (GFP); S65T, Y66(3...

ID or keywords:

Entry

Database: PDB / ID: 6un7

Title

Crystal structure of green fluorescent protein (GFP); S65T, Y66(3-OMeY); ih circular permutant (50-51)

Components

Green fluorescent protein

Keywords

FLUORESCENT PROTEIN / GFP

Function / homology

Function and homology information

bioluminescence / generation of precursor metabolites and energy
Similarity search - Function

Biological species

Aequorea victoria (jellyfish)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.5 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	Oct 10, 2019	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 14, 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 / _citation_author.name
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 / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5	Nov 20, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6un7.cif.gz	208 KB	Display	PDBx/mmCIF format
PDB format	pdb6un7.ent.gz	167.1 KB	Display	PDB format
PDBx/mmJSON format	6un7.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6un7_validation.pdf.gz	447.9 KB	Display	wwPDB validaton report
Full document	6un7_full_validation.pdf.gz	454.8 KB	Display
Data in XML	6un7_validation.xml.gz	22.6 KB	Display
Data in CIF	6un7_validation.cif.gz	31.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/un/6un7 ftp://data.pdbj.org/pub/pdb/validation_reports/un/6un7	HTTPS FTP

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Related structure data

Related structure data	6og8C 6og9C 6ogaC 6ogbC 6ogcC 6un5C 6un6C 6ofkS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	1emf-1 5vm1-3 1emk-1 2emn-1 2emd-1 6m9y-d 4ni5-4 4zf5-d 1eml-1 1emm-1 Search similar-shape structures by Omokage search (details) 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 (5)

Deposited unit

A: Green fluorescent protein

B: Green fluorescent protein

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

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	50.883, 68.601, 60.186
Angle α, β, γ (deg.)	90.00, 101.64, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Green fluorescent protein Mass: 28244.557 Da / Num. of mol.: 2 Mutation: A72S, Q80R, T105K, E111V, I128T, K166T, I167V, S205T, A206V, S232R, Y241I, C250S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: gfp, GFP / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A059PIQ0, UniProt: P42212
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 280 / 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: 1.82 Å³/Da / Density % sol: 32.49 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.15 M ammonium acetate, 34% 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: 0.97946 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 24, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97946 Å / Relative weight: 1
Reflection	Resolution: 1.5→36.141 Å / Num. obs: 63500 / % possible obs: 97.8 % / Redundancy: 13.32 % / B_iso Wilson estimate: 22.02 Å² / R_merge(I) obs: 0.056 / Net I/σ(I): 19.66
Reflection shell	Resolution: 1.5→1.54 Å / Redundancy: 13.08 % / R_merge(I) obs: 2.716 / Mean I/σ(I) obs: 1.19 / Num. unique obs: 4542 / % possible all: 95.9

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Processing

Software

Name	Version	Classification
PHENIX	1.13RC2_2986	refinement
XSCALE		data scaling
PDB_EXTRACT	3.25	data extraction
XDS		data reduction
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6OFK

6ofk

Resolution: 1.5→36.14 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 25.56

	R_factor	Num. reflection	% reflection
R_free	0.191	3171	5 %
R_work	0.167	-	-
obs	0.168	63420	97.7 %

Solvent computation

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

Displacement parameters

B_iso mean: 37.47 Å²

Refinement step

Cycle: LAST / Resolution: 1.5→36.14 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3622	0	0	281	3903

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 (%)
1.5-1.5222	0.4314	131	0.3597	2497	X-RAY DIFFRACTION	95
1.5222-1.546	0.3477	138	0.3298	2600	X-RAY DIFFRACTION	97
1.546-1.5713	0.323	130	0.2931	2495	X-RAY DIFFRACTION	93
1.5713-1.5984	0.3349	133	0.2765	2528	X-RAY DIFFRACTION	95
1.5984-1.6275	0.3094	139	0.2607	2621	X-RAY DIFFRACTION	98
1.6275-1.6588	0.2853	138	0.2393	2616	X-RAY DIFFRACTION	98
1.6588-1.6926	0.2779	138	0.2262	2632	X-RAY DIFFRACTION	98
1.6926-1.7294	0.2323	137	0.2235	2607	X-RAY DIFFRACTION	98
1.7294-1.7697	0.2876	138	0.2187	2619	X-RAY DIFFRACTION	98
1.7697-1.8139	0.2636	139	0.2043	2646	X-RAY DIFFRACTION	98
1.8139-1.863	0.227	138	0.1993	2630	X-RAY DIFFRACTION	99
1.863-1.9178	0.2229	139	0.1804	2624	X-RAY DIFFRACTION	99
1.9178-1.9797	0.1818	133	0.1685	2545	X-RAY DIFFRACTION	95
1.9797-2.0504	0.2211	139	0.1716	2640	X-RAY DIFFRACTION	99
2.0504-2.1325	0.2065	140	0.1669	2665	X-RAY DIFFRACTION	99
2.1325-2.2295	0.1405	142	0.161	2678	X-RAY DIFFRACTION	99
2.2295-2.3471	0.1873	139	0.1632	2652	X-RAY DIFFRACTION	100
2.3471-2.4941	0.177	140	0.1721	2651	X-RAY DIFFRACTION	99
2.4941-2.6866	0.2363	140	0.1708	2678	X-RAY DIFFRACTION	99
2.6866-2.9569	0.1979	135	0.1759	2553	X-RAY DIFFRACTION	95
2.9569-3.3844	0.1628	141	0.1541	2699	X-RAY DIFFRACTION	100
3.3844-4.263	0.15	144	0.1344	2702	X-RAY DIFFRACTION	100
4.263-36.141	0.1623	140	0.135	2671	X-RAY DIFFRACTION	97

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	0.4416	1.1468	-0.8263	4.1975	-0.2822	4.5845	-0.2099	-0.0603	-0.2057	-0.0473	0.05	-0.5532	0.0372	0.386	0.0933	0.1908	0.0242	0.0059	0.202	0.0071	0.2795	16.709	9.7128	0.1879
2	2.317	-3.4359	-1.1462	5.7625	1.3094	4.5256	-0.0402	-0.2681	-0.1634	0.3571	0.0775	0.5666	-0.0607	-0.306	-0.0518	0.2362	-0.012	0.054	0.2299	-0.006	0.3179	-8.5297	7.9579	7.8068
3	3.7868	2.6371	-1.4384	3.4343	-1.4025	2.0504	-0.1117	0.1807	0.1429	-0.2721	0.1599	0.066	0.1247	-0.0858	-0.0656	0.1837	0.0107	-0.0184	0.1892	0.0004	0.1975	2.133	8.9643	-4.5752
4	4.0327	3.8761	-2.5342	6.4561	-2.7461	3.5135	-0.2793	0.1767	-0.284	-0.5194	0.0885	-0.3526	0.4252	-0.0622	0.2394	0.2183	0.0127	0.031	0.1857	-0.0318	0.2308	7.7708	2.1417	-5.7096
5	2.7979	0.0037	-0.5143	1.9456	0.2113	4.2191	0.117	0.1198	0.2163	-0.074	0.058	-0.3741	-0.1206	0.5372	-0.1557	0.1757	-0.0113	-0.0087	0.2291	0.0041	0.3556	18.4908	18.9161	0.1623
6	6.771	2.8384	0.9672	3.7059	0.3371	1.1171	-0.2508	0.4588	0.1255	-0.225	0.2317	0.1584	-0.083	0.0489	0.0993	0.211	0.0076	-0.0169	0.1973	0.0123	0.2059	2.0562	17.4947	-1.7835
7	2.6932	0.9482	-0.2697	1.7746	-0.3407	1.1177	-0.271	0.2813	0.2488	-0.3844	0.2285	0.3937	0.0842	-0.2134	0.0492	0.2329	-0.0089	-0.0416	0.219	0.012	0.241	-2.9042	10.8023	-5.0262
8	3.5887	0.1513	0.3407	1.1112	0.009	1.2824	-0.07	-0.1496	-0.1443	0.1548	0.0284	-0.197	0.1301	0.1819	0.0451	0.1942	0.0234	-0.0142	0.1765	0.0028	0.264	10.864	8.8749	9.9335
9	2.0374	0.9984	0.0176	2.9566	-0.8486	1.1597	-0.0556	-0.0346	-0.2822	-0.0298	-0.0811	-0.1848	0.1237	0.033	0.1705	0.2219	0.0263	0.0041	0.1597	-0.024	0.2144	6.1332	0.913	1.849
10	2.6267	-1.9554	-2.6054	4.4686	1.1945	4.8552	-0.0695	-0.3106	-0.0009	0.1724	0.0453	-0.3927	0.1099	0.3317	0.067	0.1956	0.0179	-0.0297	0.1811	0.0035	0.2692	10.4492	2.491	8.2315
11	5.6281	-0.8123	-1.1212	1.7255	-0.2577	2.5742	-0.2913	-0.6538	-0.2768	0.1812	0.1645	-0.1115	0.2358	0.5717	0.1276	0.3292	0.0972	0.0218	0.356	0.038	0.1909	14.9493	18.7182	26.1294
12	4.1603	-0.5859	1.1035	1.2694	-0.8406	3.5096	-0.1088	-0.6429	0.18	0.1832	0.1696	-0.2258	-0.1869	0.7866	0.1169	0.3973	0.0916	-0.0221	0.5477	-0.0383	0.182	16.3409	25.2629	31.819
13	1.9816	-0.0361	1.5558	0.4138	-0.646	2.1472	-0.4169	-1.2438	0.1272	0.5021	0.3502	-0.0252	0.0305	0.5282	0.0353	0.5321	0.2639	0.0617	0.7414	0.0969	0.1578	11.0508	21.5854	37.7417
14	4.2946	-0.2642	0.0416	4.1482	1.0555	4.1715	0.121	0.0411	0.1207	0.1004	-0.0558	0.3223	-0.5086	-0.5341	-0.0597	0.322	0.0675	0.0319	0.2664	0.0859	0.2246	-0.8158	26.9992	21.789
15	3.732	-1.4288	1.1943	2.6738	-0.1514	2.6969	-0.1434	-0.5013	0.4871	0.1621	0.1971	-0.4089	-0.321	0.2552	-0.0151	0.3664	-0.0478	0.0229	0.337	-0.0692	0.2447	15.4599	29.3384	23.2376
16	1.3384	0.7863	-0.9507	1.3112	0.485	1.9292	-0.1301	-0.4274	0.2985	0.3713	0.097	-0.4429	-0.2891	0.8636	0.0942	0.4074	-0.0012	-0.0549	0.5676	-0.0814	0.265	20.355	28.0159	30.0508
17	3.2815	0.1767	-1.3059	1.4555	-0.0408	2.5996	-0.2886	-0.0894	-0.1765	0.2367	0.147	0.1996	0.4779	0.0166	0.1228	0.3165	0.0146	0.0498	0.2079	0.0415	0.2506	8.6738	13.9417	22.0222
18	0.6815	-0.5608	0.8943	2.073	-1.1098	3.6629	-0.3461	-0.6053	-0.376	0.3673	0.1181	-0.451	0.5393	1.3473	0.5703	0.5831	0.3746	0.0949	0.9829	0.1792	0.5563	31.0643	13.7694	27.6697
19	0.7304	-0.249	0.9763	2.1707	-1.3237	1.8204	-0.3773	-0.6539	-0.3463	0.3943	0.0233	0.2891	0.3121	0.196	-0.5856	0.5107	0.2503	0.172	0.5144	0.267	0.3181	5.1838	16.3865	35.119
20	4.7243	-0.522	-3.8409	2.4433	0.6315	4.2409	-0.6964	-0.8117	-0.5434	0.2697	0.3048	0.1921	0.6366	0.3131	0.1029	0.4843	0.1236	0.1032	0.3715	0.1322	0.3109	9.2882	11.0827	28.1776

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN 'A' AND (RESID 1 THROUGH 18 )
2	X-RAY DIFFRACTION	2	CHAIN 'A' AND (RESID 19 THROUGH 31 )
3	X-RAY DIFFRACTION	3	CHAIN 'A' AND (RESID 32 THROUGH 54 )
4	X-RAY DIFFRACTION	4	CHAIN 'A' AND (RESID 55 THROUGH 78 )
5	X-RAY DIFFRACTION	5	CHAIN 'A' AND (RESID 79 THROUGH 98 )
6	X-RAY DIFFRACTION	6	CHAIN 'A' AND (RESID 99 THROUGH 125 )
7	X-RAY DIFFRACTION	7	CHAIN 'A' AND (RESID 126 THROUGH 148 )
8	X-RAY DIFFRACTION	8	CHAIN 'A' AND (RESID 149 THROUGH 177 )
9	X-RAY DIFFRACTION	9	CHAIN 'A' AND (RESID 178 THROUGH 229 )
10	X-RAY DIFFRACTION	10	CHAIN 'A' AND (RESID 230 THROUGH 243 )
11	X-RAY DIFFRACTION	11	CHAIN 'B' AND (RESID 1 THROUGH 31 )
12	X-RAY DIFFRACTION	12	CHAIN 'B' AND (RESID 32 THROUGH 54 )
13	X-RAY DIFFRACTION	13	CHAIN 'B' AND (RESID 55 THROUGH 78 )
14	X-RAY DIFFRACTION	14	CHAIN 'B' AND (RESID 79 THROUGH 98 )
15	X-RAY DIFFRACTION	15	CHAIN 'B' AND (RESID 99 THROUGH 125 )
16	X-RAY DIFFRACTION	16	CHAIN 'B' AND (RESID 126 THROUGH 148 )
17	X-RAY DIFFRACTION	17	CHAIN 'B' AND (RESID 149 THROUGH 177 )
18	X-RAY DIFFRACTION	18	CHAIN 'B' AND (RESID 178 THROUGH 204 )
19	X-RAY DIFFRACTION	19	CHAIN 'B' AND (RESID 205 THROUGH 229 )
20	X-RAY DIFFRACTION	20	CHAIN 'B' AND (RESID 230 THROUGH 243 )

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