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- PDB-8aab: S148F mutant of blue-to-red fluorescent timer mRubyFT -

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Basic information

Entry
Database: PDB / ID: 8aab
TitleS148F mutant of blue-to-red fluorescent timer mRubyFT
ComponentsmRubyFT S148F mutant of blue-to-red fluorescent timer
KeywordsFLUORESCENT PROTEIN / mRubyFT / S148I mutant / flourescent 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: 1.6 Å
AuthorsBoyko, K.M. / Nikolaeva, A.Y. / Vlaskina, A.V. / Dorovatovskii, P.V. / Subach, O.M. / Popov, V.O. / Subach, F.V.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Science Foundation21-74-20135 Russian Federation
CitationJournal: Crystallography Reports / Year: 2022
Title: mRubyFT/S147I, a mutant of blue-to-red fluorescent timer
Authors: Boyko, K.M. / Nikolaeva, A.Y. / Dorovatovskii, P.V. / Vlaskina, A.V. / Subach, O.M. / Subach, F.V.
History
DepositionJun 30, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 17, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2022Group: Database references / Category: citation
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.title / _citation.year
Revision 1.2Apr 12, 2023Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.3Feb 7, 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
A: mRubyFT S148F mutant of blue-to-red fluorescent timer


Theoretical massNumber of molelcules
Total (without water)27,0981
Polymers27,0981
Non-polymers00
Water2,216123
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9810 Å2
Unit cell
Length a, b, c (Å)31.524, 66.465, 96.488
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 S148F mutant of blue-to-red fluorescent timer / GFP-like chromoprotein


Mass: 27098.084 Da / Num. of mol.: 1 / Mutation: S148F
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 / Water


Mass: 18.015 Da / Num. of mol.: 123 / Source method: isolated from a natural source / Formula: H2O

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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: 1.87 Å3/Da / Density % sol: 34.05 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / Details: 250 mM MgCl2; 100 mM HEPES 20% PEG 3350, pH 7,5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: KURCHATOV SNC / Beamline: K4.4 / Wavelength: 0.79373 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 27, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.79373 Å / Relative weight: 1
ReflectionResolution: 1.55→31.42 Å / Num. obs: 30195 / % possible obs: 99.7 % / Redundancy: 4.9 % / CC1/2: 0.995 / Rmerge(I) obs: 0.127 / Rpim(I) all: 0.064 / Rrim(I) all: 0.143 / Net I/σ(I): 7 / Num. measured all: 149362 / Scaling rejects: 169
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
1.55-1.585.10.95751614840.5010.461.0591.5100
8.49-31.423.90.0438512210.9930.0260.0515.797.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.7.8data scaling
MOLREPphasing
REFMAC5.8.0352refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7QGK

7qgk


Resolution: 1.6→31.42 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.942 / SU B: 4.818 / SU ML: 0.081 / SU R Cruickshank DPI: 0.1007 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.101 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2203 1350 4.9 %RANDOM
Rwork0.1936 ---
obs0.195 26111 99.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 51.34 Å2 / Biso mean: 16.126 Å2 / Biso min: 8.11 Å2
Baniso -1Baniso -2Baniso -3
1--0.45 Å2-0 Å2-0 Å2
2---0.82 Å20 Å2
3---1.27 Å2
Refinement stepCycle: final / Resolution: 1.6→31.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1720 0 0 123 1843
Biso mean---23.35 -
Num. residues----219
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0121812
X-RAY DIFFRACTIONr_bond_other_d0.0060.0161637
X-RAY DIFFRACTIONr_angle_refined_deg1.9141.6522450
X-RAY DIFFRACTIONr_angle_other_deg0.9281.5533830
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4445224
X-RAY DIFFRACTIONr_dihedral_angle_2_deg16.5621012
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.89610313
X-RAY DIFFRACTIONr_chiral_restr0.1040.2261
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022062
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02378
LS refinement shellResolution: 1.6→1.641 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 72 -
Rwork0.293 1929 -
all-2001 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 29.7536 Å / Origin y: 57.7583 Å / Origin z: 21.9898 Å
111213212223313233
T0.0029 Å20.0013 Å2-0.0015 Å2-0.0113 Å2-0.001 Å2--0.0241 Å2
L0.5223 °2-0.0513 °20.0124 °2-0.4328 °20.0949 °2--0.8411 °2
S-0.0155 Å °-0.0258 Å °-0.004 Å °0.0285 Å °-0.0155 Å °-0.019 Å °0.0277 Å °0.0346 Å °0.0311 Å °

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