PDB-8arm: Crystal structure of LSSmScarlet2

ID or keywords:

Entry

Database: PDB / ID: 8arm

Title

Crystal structure of LSSmScarlet2

Components

LSSmScarlet2

Keywords

FLUORESCENT PROTEIN / LSSmScarlet2

Function / homology

Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / generation of precursor metabolites and energy / Red fluorescent protein drFP583

Function and homology information

Biological species

Discosoma sp. (sea anemone)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.41 Å

Authors

Samygina, V.R. / Subach, O.M. / Vlaskina, A.V. / Subach, F.V.

Funding support

Russian Federation, 1items

Citation

Journal: Int J Mol Sci / Year: 2022
Title: LSSmScarlet2 and LSSmScarlet3, Chemically Stable Genetically Encoded Red Fluorescent Proteins with a Large Stokes' Shift.
Authors: Subach, O.M. / Vlaskina, A.V. / Agapova, Y.K. / Piatkevich, K.D. / Patrushev, M.V. / Samygina, V.R. / Subach, F.V.

History

Deposition	Aug 17, 2022	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Nov 2, 2022	Provider: repository / Type: Initial release
Revision 1.1	Jan 31, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8arm.cif.gz	118.1 KB	Display	PDBx/mmCIF format
PDB format	pdb8arm.ent.gz	86.8 KB	Display	PDB format
PDBx/mmJSON format	8arm.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/ar/8arm ftp://data.pdbj.org/pub/pdb/validation_reports/ar/8arm	HTTPS FTP

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Related structure data

Related structure data	5lk4S S: Starting model for refinement
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)

Deposited unit

A: LSSmScarlet2

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	84.618, 45.373, 58.744
Angle α, β, γ (deg.)	90.000, 102.092, 90.000
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	A-475- HOH
2	1	A-668- HOH

#1: Protein	LSSmScarlet2 Mass: 26513.982 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Discosoma sp. (sea anemone) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9U6Y8
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 381 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	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: 2.08 Å³/Da / Density % sol: 40.8 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG3350, MES pH6.0

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.967697 Å
Detector	Type: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Dec 5, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.967697 Å / Relative weight: 1
Reflection	Resolution: 1.41→39.8 Å / Num. obs: 42307 / % possible obs: 97.57 % / Redundancy: 1.56 % / B_iso Wilson estimate: 17.61 Å² / CC_1/2: 1 / Net I/σ(I): 15.5
Reflection shell	Resolution: 1.41→1.45 Å / Mean I/σ(I) obs: 4.43 / Num. unique obs: 2725 / CC_1/2: 0.94 / R_rim(I) all: 0.26

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0257	refinement
XDS		data reduction
Aimless		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5LK4

5lk4

Resolution: 1.41→15 Å / Cor.coef. F_o:F_c: 0.979 / Cor.coef. F_o:F_c free: 0.968 / SU B: 1.713 / SU ML: 0.03 / Cross valid method: FREE R-VALUE / ESU R: 0.057 / ESU R Free: 0.053
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1523	2090	5.091 %
R_work	0.1125	38959	-
all	0.115	-	-
obs	-	41049	97.402 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 12.017 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.432 Å²	-0 Å²	0.496 Å²
2-	-	0.304 Å²	-0 Å²
3-	-	-	-0.077 Å²

Refinement step

Cycle: LAST / Resolution: 1.41→15 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1738	0	28	381	2147

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.013	1956
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	1825
X-RAY DIFFRACTION	r_angle_refined_deg	1.752	1.684	2656
X-RAY DIFFRACTION	r_angle_other_deg	1.422	1.599	4277
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.269	5	257
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	30.791	21.429	112
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.059	15	369
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.234	15	17
X-RAY DIFFRACTION	r_chiral_restr	0.081	0.2	241
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	2222
X-RAY DIFFRACTION	r_gen_planes_other	0.003	0.02	433
X-RAY DIFFRACTION	r_nbd_refined	0.241	0.2	353
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.203	0.2	1630
X-RAY DIFFRACTION	r_nbtor_refined	0.167	0.2	864
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.088	0.2	937
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.162	0.2	248
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.071	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.244	0.2	14
X-RAY DIFFRACTION	r_nbd_other	0.174	0.2	39
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.146	0.2	47
X-RAY DIFFRACTION	r_mcbond_it	1.054	0.847	922
X-RAY DIFFRACTION	r_mcbond_other	0.985	0.84	920
X-RAY DIFFRACTION	r_mcangle_it	1.298	1.276	1162
X-RAY DIFFRACTION	r_mcangle_other	1.303	1.275	1162
X-RAY DIFFRACTION	r_scbond_it	1.56	1.173	1034
X-RAY DIFFRACTION	r_scbond_other	1.558	1.169	1031
X-RAY DIFFRACTION	r_scangle_it	1.869	1.636	1475
X-RAY DIFFRACTION	r_scangle_other	1.864	1.629	1469
X-RAY DIFFRACTION	r_lrange_it	4.222	13.602	2291
X-RAY DIFFRACTION	r_lrange_other	3.323	12.074	2179
X-RAY DIFFRACTION	r_rigid_bond_restr	1.371	3	3780

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.41-1.446	0.207	151	0.156	2609	0.159	3040	0.941	0.953	90.7895	0.144
1.446-1.486	0.161	146	0.132	2773	0.133	2995	0.961	0.968	97.4624	0.121
1.486-1.528	0.154	142	0.118	2707	0.12	2888	0.967	0.974	98.6496	0.108
1.528-1.575	0.177	149	0.109	2670	0.112	2858	0.957	0.969	98.6354	0.099
1.575-1.626	0.151	130	0.099	2582	0.102	2742	0.968	0.975	98.9059	0.089
1.626-1.682	0.143	137	0.085	2519	0.087	2682	0.971	0.983	99.0306	0.078
1.682-1.745	0.14	122	0.094	2401	0.096	2555	0.973	0.98	98.7476	0.085
1.745-1.815	0.147	114	0.086	2320	0.089	2473	0.974	0.985	98.423	0.079
1.815-1.894	0.137	124	0.094	2210	0.096	2370	0.974	0.983	98.481	0.089
1.894-1.985	0.131	109	0.099	2118	0.101	2273	0.977	0.982	97.9762	0.095
1.985-2.091	0.15	106	0.095	2040	0.098	2188	0.979	0.987	98.0804	0.093
2.091-2.215	0.126	114	0.099	1890	0.101	2039	0.983	0.985	98.2835	0.099
2.215-2.364	0.143	108	0.098	1783	0.1	1951	0.972	0.981	96.9247	0.099
2.364-2.548	0.139	90	0.1	1551	0.103	1812	0.977	0.981	90.5629	0.104
2.548-2.783	0.164	92	0.117	1544	0.12	1650	0.966	0.977	99.1515	0.123
2.783-3.099	0.145	73	0.117	1444	0.119	1538	0.976	0.978	98.6346	0.127
3.099-3.553	0.12	53	0.108	1266	0.108	1342	0.985	0.985	98.2861	0.121
3.553-4.291	0.162	52	0.123	1100	0.125	1169	0.971	0.975	98.5458	0.144
4.291-5.835	0.192	43	0.158	872	0.159	928	0.979	0.981	98.5991	0.192
5.835-15	0.225	34	0.243	550	0.242	599	0.953	0.957	97.4958	0.293

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