PDB-4ljd: Structure of a photobleached state of IrisFP under low intensity ...

ID or keywords:

Entry

Database: PDB / ID: 4ljd

Title

Structure of a photobleached state of IrisFP under low intensity laser-light

Components

(Green to red photoconvertible GPF-like protein EosFP) x 2

Keywords

FLUORESCENT PROTEIN /

Photobleaching /

Beta-Barrel /

Oxidation

Function / homology

Function and homology information

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

Biological species

Lobophyllia hemprichii (invertebrata)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.5 Å

Authors

Duan, C. / Adam, V. / Byrdin, M. / Ridard, J. / Kieffer-Jacquinod, S. / Morlot, C. / Arcizet, D. / Demachy, I. / Bourgeois, D.

Citation

Journal: J.Am.Chem.Soc. / Year: 2013
Title: Structural evidence for a two-regime photobleaching mechanism in a reversibly switchable fluorescent protein.
Authors: Duan, C. / Adam, V. / Byrdin, M. / Ridard, J. / Kieffer-Jaquinod, S. / Morlot, C. / Arcizet, D. / Demachy, I. / Bourgeois, D.

History

Deposition	Jul 4, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 9, 2013	Provider: repository / Type: Initial release
Revision 1.1	Nov 6, 2013	Group: Database references
Revision 2.0	Nov 15, 2023	Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / database_2 / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / struct_conn / struct_ref_seq_dif / struct_site Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4ljd.cif.gz	361.8 KB	Display	PDBx/mmCIF format
PDB format	pdb4ljd.ent.gz	295.8 KB	Display	PDB format
PDBx/mmJSON format	4ljd.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/lj/4ljd ftp://data.pdbj.org/pub/pdb/validation_reports/lj/4ljd	HTTPS FTP

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Related structure data

Related structure data	4ljbC 4ljcC 2vvh 2vvi 2vvj 3tmr 3tmt C: citing same article (ref.)
Similar structure data	4r6b-d 1zux-d 4ljb-d 3s05-d 6nqp-2 4ljc-d 2vvi-d 2vvh-d 2gx0-d 1zgo-d 1zgq-2 4dxi-d 2h8q-1 4izn-2 3p8u-d 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 (4) #42 - Jun 2003 Green Fluorescent Protein similarity (4) #133 - Jan 2011 Nitric Oxide Synthase similarity (1)

Deposited unit

A: Green to red photoconvertible GPF-like protein EosFP

B: Green to red photoconvertible GPF-like protein EosFP

C: Green to red photoconvertible GPF-like protein EosFP

D: Green to red photoconvertible GPF-like protein EosFP

hetero molecules

107 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	85.906, 96.487, 140.136
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 GPF-like protein EosFP Mass: 26188.557 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lobophyllia hemprichii (invertebrata) / Production host: Escherichia coli (E. coli) / References: UniProt: Q5S6Z9
#2: Protein	Green to red photoconvertible GPF-like protein EosFP Mass: 26172.557 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lobophyllia hemprichii (invertebrata) / Production host: Escherichia coli (E. coli) / References: UniProt: Q5S6Z9
#3: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: SO₄
#4: Chemical	ChemComp-SO3 / SULFITE ION / Sulfite Mass: 80.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO₃
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 423 / 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: 2.77 Å³/Da / Density % sol: 55.64 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 2.1M ammonium sulfate, 0.1M bicine, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99979 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 22, 2012
Radiation	Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.99979 Å / Relative weight: 1
Reflection	Resolution: 2.5→47.34 Å / Num. all: 75076 / Num. obs: 40184 / % possible obs: 97.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.4 % / B_iso Wilson estimate: 55.6 Å² / R_sym value: 0.075 / Net I/σ(I): 11.8
Reflection shell	Resolution: 2.5→2.64 Å / % possible all: 97.5

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Processing

Software

Name	Version	Classification
DA+		data collection
MOLREP		phasing
PHENIX	(phenix.refine: 1.8.2_1309)	refinement
XDS		data reduction
SCALA		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.5→45.616 Å / SU ML: 0.43 / σ(F): 1.35 / Phase error: 29.67 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2559	2048	5.1 %
R_work	0.1993	-	-
obs	0.2022	40184	97.95 %
all	-	40198	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.5→45.616 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7143	0	96	423	7662

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	7433
X-RAY DIFFRACTION	f_angle_d	0.93	10026
X-RAY DIFFRACTION	f_dihedral_angle_d	14.072	2721
X-RAY DIFFRACTION	f_chiral_restr	0.05	1016
X-RAY DIFFRACTION	f_plane_restr	0.004	1287

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 (%)
2.5-2.5582	0.4019	156	0.3016	2474	X-RAY DIFFRACTION	98
2.5582-2.6222	0.3571	135	0.2999	2508	X-RAY DIFFRACTION	97
2.6222-2.693	0.3865	143	0.2882	2481	X-RAY DIFFRACTION	98
2.693-2.7723	0.3866	133	0.2801	2511	X-RAY DIFFRACTION	98
2.7723-2.8618	0.3337	122	0.2591	2507	X-RAY DIFFRACTION	98
2.8618-2.964	0.3149	136	0.2631	2489	X-RAY DIFFRACTION	97
2.964-3.0827	0.3354	127	0.2683	2497	X-RAY DIFFRACTION	96
3.0827-3.2229	0.3131	138	0.2298	2513	X-RAY DIFFRACTION	97
3.2229-3.3928	0.2741	142	0.2073	2521	X-RAY DIFFRACTION	99
3.3928-3.6053	0.2315	141	0.1882	2544	X-RAY DIFFRACTION	98
3.6053-3.8835	0.2139	106	0.1753	2585	X-RAY DIFFRACTION	98
3.8835-4.2741	0.2233	142	0.1598	2569	X-RAY DIFFRACTION	99
4.2741-4.8919	0.175	132	0.1399	2578	X-RAY DIFFRACTION	98
4.8919-6.1609	0.189	148	0.1609	2638	X-RAY DIFFRACTION	99
6.1609-45.6236	0.239	147	0.1876	2721	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	0.0028	0.0021	-0.0004	0.001	-0.0006	-0	-0.0066	0.0006	0.0141	-0.007	-0.0034	0.0055	0.0045	-0.0031	0	0.0422	-0.0019	-0.0409	0.0635	-0.0396	0.1078	-54.6251	-13.1275	-39.4807
2	0.0063	-0.0107	-0.0035	0.0094	0.0033	0.0097	-0.0013	-0.019	-0.029	0.0065	-0.0354	0.0115	-0.019	0.0308	-0	0.0433	0.0305	-0.0093	-0.0087	-0.0239	0.0537	-45.438	-8.2998	-35.332
3	0.0129	-0.0001	0.0001	0.0048	0.0057	0.0063	-0.0216	0.0106	0.0195	-0.0135	0.0258	0.0302	0.0025	0.0035	0	0.0905	0.0767	0.012	0.0201	-0.0097	0.0681	-41.83	-13.4857	-38.1585
4	0.0045	-0.0045	0.002	-0.0061	0.0021	0.0001	-0.0106	0.0038	-0.0013	0.0027	0.0121	-0.0313	0.0036	0.0031	-0	-0.108	0.1555	0.0459	0.1833	-0.0672	0.0497	-6.0048	-15.589	-27.0451
5	0.0056	0.0018	-0.0008	-0.0015	-0.0034	0.001	0.0334	0.022	-0.0198	0.0178	0.041	-0.0596	0.0273	0.0371	0	-0.1681	-0.0379	-0.0041	0.1237	-0.0212	0.0593	-13.9558	-10.4007	-26.2198
6	0.0006	0.0004	0.001	0.0008	0.0017	0.0012	0.0128	0.0219	-0.0076	0.0037	0.0036	-0.0066	0.0084	0.0129	0	0.0756	0.0367	-0.0565	0.0748	0.0328	0.0806	-25.703	-12.6253	-27.0129
7	0.0019	0	0.0008	-0.0017	-0.0004	-0.0001	-0.009	-0.0023	-0.0036	-0.0059	0.0036	-0.0055	-0.0102	0.0018	0	-0.0011	-0.006	-0.029	0.0662	0.0484	0.0734	-16.06	0.5853	-36.0506
8	0.0014	-0.0001	-0.0022	0.0009	0.0009	0.002	-0.0031	0.0014	-0.0186	-0.0032	0.0032	-0.0062	0.0003	0.0049	0	0.0372	0.0564	0.0024	0.0525	0.025	0.0674	-18.7743	-19.5165	-31.6317
9	-0.0024	-0.0014	0.0008	0.0031	0.0033	0.0012	0.0011	0.0095	0.0049	-0.0092	0.0206	-0.0097	0.0002	0.0026	-0	0.0845	0.0294	0.0019	0.033	-0.033	0.0175	-17.4235	-20.0739	-31.396
10	0.0005	0.0011	-0.0036	-0.0004	0.0023	-0.0014	0.008	-0.0054	0.002	-0.0021	0.0053	0.0232	-0.0079	-0.0115	0	0.0157	-0.0368	0.0788	0.0597	0.0341	0.0672	-60.4101	7.4076	-10.4245
11	-0.0004	0.0057	-0.0129	0.0064	0.0049	0.0119	-0.1267	-0.0223	0.0679	0.0707	-0.1359	0.0733	-0.1051	-0.084	-0	-0.0096	-0.0551	0.1332	-0.0153	0.0724	-0.0778	-49.3518	5.2412	-10.1909
12	0.0024	-0.0043	-0.0051	0.0029	0.0035	0.0032	0.0175	-0.0164	0.0158	0.0035	0.041	-0.0194	0.0036	-0.0011	0	0.0883	-0.0366	0.0517	0.07	-0.0075	0.0719	-50.0232	4.5209	-0.6681
13	0.0017	-0.0008	-0.0016	-0.0086	0	-0.0007	0.0059	-0.0054	0.0134	0.0377	-0.0021	-0.0171	0.0109	0.0071	-0	-0.1793	-0.0376	-0.0934	0.0618	0.0225	-0.0092	-12.22	9.8547	-3.3396
14	-0.0069	0.001	0.0017	0.0022	0.0081	0.0058	0.0295	-0.0145	0.014	0.0315	0.0137	-0.0663	0.0211	0.0167	-0	0.0095	-0.0913	-0.0941	-0.0524	0.0129	-0.1247	-22.4446	4.1005	-5.3758
15	-0.0023	0.0022	-0.0009	-0.0006	0.0078	0.0043	-0.0319	-0.0256	-0.0013	-0.0014	0.0035	-0.0042	-0.0191	-0.0153	0	0.065	-0.0396	0.0166	0.0354	-0.038	-0.0814	-24.188	9.3934	0.1718

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 20 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 21 through 172 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 173 through 223 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 2 through 46 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 47 through 135 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 136 through 172 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 173 through 189 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 190 through 201 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 202 through 223 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid -1 through 32 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 33 through 201 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 202 through 223 )
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 1 through 60 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 61 through 179 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 180 through 223 )

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