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- PDB-7q6b: mRubyFT/S148I, a mutant of blue-to-red fluorescent timer in its b... -

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Entry
Database: PDB / ID: 7q6b
TitlemRubyFT/S148I, a mutant of blue-to-red fluorescent timer in its blue state
ComponentsmRubyFT S148I, a mutant of blue-to-red fluorescent timer
KeywordsFLUORESCENT PROTEIN / mRubyFT / mRuby / blue color fluorescent protein / cell timer / fluorescent timer
Function / homologyGreen fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / Red fluorescent protein eqFP611
Function and homology information
Biological speciesEntacmaea quadricolor (sea anemone)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsBoyko, K.M. / Nikolaeva, A.Y. / Vlaskina, A.V. / Dorovatovskii, P.V. / Khrenova, M.G. / Subach, O.M. / Popov, V.O. / Subach, F.M.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Science Foundation21-74-20135 Russian Federation
CitationJournal: Int J Mol Sci / Year: 2023
Title: Combined Structural and Computational Study of the mRubyFT Fluorescent Timer Locked in Its Blue Form.
Authors: Boyko, K.M. / Khrenova, M.G. / Nikolaeva, A.Y. / Dorovatovskii, P.V. / Vlaskina, A.V. / Subach, O.M. / Popov, V.O. / Subach, F.V.
History
DepositionNov 6, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 12, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2023Group: Structure summary / Category: entity / struct / Item: _entity.pdbx_description / _struct.title
Revision 1.2Oct 25, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / struct_conn
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 / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id
Revision 2.1Feb 7, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: mRubyFT S148I, a mutant of blue-to-red fluorescent timer


Theoretical massNumber of molelcules
Total (without water)27,0441
Polymers27,0441
Non-polymers00
Water1,36976
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.790, 66.828, 97.762
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein mRubyFT S148I, a mutant of blue-to-red fluorescent timer / GFP-like chromoprotein


Mass: 27044.035 Da / Num. of mol.: 1 / Mutation: S147I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Entacmaea quadricolor (sea anemone) / Production host: Escherichia coli (E. coli) / References: UniProt: Q8ISF8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 1.93 Å3/Da / Density % sol: 26.09 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.1M Bis-tris pH 5.5; 19% 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: 0.79312 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 11, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.79312 Å / Relative weight: 1
ReflectionResolution: 1.8→48.88 Å / Num. obs: 19640 / % possible obs: 98.2 % / Redundancy: 4.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.039 / Rrim(I) all: 0.09 / Net I/σ(I): 6.1 / Num. measured all: 96802
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
1.8-1.845.21.2580511160.5140.5761.3340.296.7
9-48.883.90.0276671710.9980.0150.03154.186.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.7.7data scaling
MOLREPphasing
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
DIALSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3U0L

3u0l


Resolution: 1.8→48.88 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.933 / SU B: 17.865 / SU ML: 0.234 / SU R Cruickshank DPI: 0.1692 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.169 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2666 974 5 %RANDOM
Rwork0.2271 ---
obs0.2291 18638 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: 91.52 Å2 / Biso mean: 37.179 Å2 / Biso min: 16.36 Å2
Baniso -1Baniso -2Baniso -3
1-0.63 Å20 Å2-0 Å2
2---0.44 Å20 Å2
3----0.19 Å2
Refinement stepCycle: final / Resolution: 1.8→48.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1760 0 489 76 2325
Biso mean--41.63 37.08 -
Num. residues----158
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0131807
X-RAY DIFFRACTIONr_bond_other_d0.0030.0151688
X-RAY DIFFRACTIONr_angle_refined_deg2.1031.672428
X-RAY DIFFRACTIONr_angle_other_deg1.2991.5983903
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.8315219
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.84322.06592
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.76815317
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8881511
X-RAY DIFFRACTIONr_chiral_restr0.0890.2222
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022020
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02415
LS refinement shellResolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 66 -
Rwork0.378 1364 -
all-1430 -
obs--98.55 %
Refinement TLS params.Method: refined / Origin x: -14.401 Å / Origin y: -7.986 Å / Origin z: -21.543 Å
111213212223313233
T0.0801 Å20.0196 Å20.0021 Å2-0.1132 Å20.0341 Å2--0.0191 Å2
L0.9887 °20.4611 °20.0055 °2-2.0497 °2-1.1893 °2--3.0375 °2
S-0.0738 Å °0.2633 Å °0.1176 Å °0.0953 Å °0.0022 Å °0.0924 Å °0.012 Å °0.132 Å °0.0716 Å °

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