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- PDB-7oin: Crystal structure of LSSmScarlet - a genetically encoded red fluo... -

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Entry
Database: PDB / ID: 7oin
TitleCrystal structure of LSSmScarlet - a genetically encoded red fluorescent protein with a large Stokes shift
ComponentsLSSmScarlet - Genetically Encoded Red Fluorescent Proteins with a Large Stokes Shift
KeywordsFLUORESCENT PROTEIN / mScarlet
Function / homologyGreen 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 speciesDiscosoma sp. (sea anemone)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4 Å
AuthorsBoyko, K.M. / Nikolaeva, A.Y. / Dorovatovskii, P.V. / Subach, O.M. / Vlaskina, A.V. / Agapova, Y.K. / Ivashkina, O.I. / Popov, V.O. / Subach, F.V.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Science Foundation21-74-20135 Russian Federation
CitationJournal: Int J Mol Sci / Year: 2021
Title: LSSmScarlet, dCyRFP2s, dCyOFP2s and CRISPRed2s, Genetically Encoded Red Fluorescent Proteins with a Large Stokes Shift.
Authors: Subach, O.M. / Vlaskina, A.V. / Agapova, Y.K. / Dorovatovskii, P.V. / Nikolaeva, A.Y. / Ivashkina, O.I. / Popov, V.O. / Piatkevich, K.D. / Khrenova, M.G. / Smirnova, T.A. / Boyko, K.M. / Subach, F.V.
History
DepositionMay 12, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 16, 2022Provider: repository / Type: Initial release
Revision 2.0Sep 14, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_mod_residue / pdbx_struct_sheet_hbond / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_torsion / struct_asym / struct_conf / struct_conn / struct_mon_prot_cis / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_sheet_range
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity_poly.nstd_monomer / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_strand_id / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_sheet_hbond.range_1_auth_asym_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_asym_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_struct_special_symmetry.auth_asym_id / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_seq_id / _pdbx_validate_rmsd_angle.auth_asym_id_1 / _pdbx_validate_rmsd_angle.auth_asym_id_2 / _pdbx_validate_rmsd_angle.auth_asym_id_3 / _pdbx_validate_rmsd_angle.auth_seq_id_1 / _pdbx_validate_rmsd_angle.auth_seq_id_2 / _pdbx_validate_rmsd_angle.auth_seq_id_3 / _pdbx_validate_rmsd_bond.auth_asym_id_1 / _pdbx_validate_rmsd_bond.auth_asym_id_2 / _pdbx_validate_rmsd_bond.auth_seq_id_1 / _pdbx_validate_rmsd_bond.auth_seq_id_2 / _pdbx_validate_torsion.auth_asym_id / _pdbx_validate_torsion.auth_seq_id / _struct_conf.beg_auth_asym_id / _struct_conf.beg_auth_seq_id / _struct_conf.beg_label_seq_id / _struct_conf.end_auth_asym_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_seq_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_mon_prot_cis.auth_asym_id / _struct_mon_prot_cis.auth_seq_id / _struct_mon_prot_cis.label_seq_id / _struct_mon_prot_cis.pdbx_auth_asym_id_2 / _struct_mon_prot_cis.pdbx_auth_seq_id_2 / _struct_mon_prot_cis.pdbx_label_seq_id_2 / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.pdbx_strand_id / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end / _struct_sheet_range.beg_auth_asym_id / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_auth_asym_id / _struct_sheet_range.end_auth_seq_id / _struct_sheet_range.end_label_seq_id
Revision 2.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: LSSmScarlet - Genetically Encoded Red Fluorescent Proteins with a Large Stokes Shift
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2344
Polymers31,0921
Non-polymers1423
Water4,900272
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1190 Å2
ΔGint-32 kcal/mol
Surface area10880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.519, 45.357, 59.042
Angle α, β, γ (deg.)90.000, 102.340, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-446-

HOH

21B-608-

HOH

31B-641-

HOH

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Components

#1: Protein LSSmScarlet - Genetically Encoded Red Fluorescent Proteins with a Large Stokes Shift


Mass: 31091.904 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: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 272 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.78 Å3/Da / Density % sol: 30.77 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop
Details: 0.1M Lithium sulfate, 0.1M Ammonium acetate, 0.1 M Bis-tris pH 6.5, 23% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: KURCHATOV SNC / Beamline: K4.4 / Wavelength: 0.75 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Apr 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.75 Å / Relative weight: 1
ReflectionResolution: 1.4→34.43 Å / Num. obs: 42242 / % possible obs: 98 % / Redundancy: 6 % / CC1/2: 0.991 / Rmerge(I) obs: 0.137 / Rpim(I) all: 0.06 / Rrim(I) all: 0.15 / Net I/σ(I): 7.2 / Num. measured all: 252698 / Scaling rejects: 107
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.4-1.426.20.6151316121370.8130.2680.6721.7100
7.67-34.435.50.05914932720.9970.0270.06515.195.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimless0.7.4data scaling
MOLREPphasing
PDB_EXTRACT3.27data extraction
DIALSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LK4
Resolution: 1.4→34.43 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.954 / WRfactor Rfree: 0.1865 / WRfactor Rwork: 0.1586 / FOM work R set: 0.8665 / SU B: 1.223 / SU ML: 0.048 / SU R Cruickshank DPI: 0.0612 / SU Rfree: 0.0629 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.061 / ESU R Free: 0.063 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1896 2021 4.8 %RANDOM
Rwork0.1635 ---
obs0.1648 40220 97.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 48.75 Å2 / Biso mean: 10.778 Å2 / Biso min: 4.67 Å2
Baniso -1Baniso -2Baniso -3
1--0.46 Å2-0 Å2-0.31 Å2
2---0.09 Å20 Å2
3---0.63 Å2
Refinement stepCycle: final / Resolution: 1.4→34.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1778 0 30 272 2080
Biso mean--7.75 21.39 -
Num. residues----226
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0131922
X-RAY DIFFRACTIONr_bond_other_d0.0070.0171797
X-RAY DIFFRACTIONr_angle_refined_deg2.1641.6722590
X-RAY DIFFRACTIONr_angle_other_deg1.5721.594162
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8425227
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.38721.404114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.35515347
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4781516
X-RAY DIFFRACTIONr_chiral_restr0.1250.2242
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.022135
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02437
LS refinement shellResolution: 1.4→1.436 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 159 -
Rwork0.254 2994 -
all-3153 -
obs--100 %

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