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- PDB-7zct: Structure of the red fluorescent protein mScarlet3 at pH 7.5 -

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Basic information

Entry
Database: PDB / ID: 7zct
TitleStructure of the red fluorescent protein mScarlet3 at pH 7.5
ComponentsRed fluorescent protein drFP583
KeywordsFLUORESCENT PROTEIN / Red fluorescent protein / high fluorescence quantum yield / efficient chromophore maturation
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 / Resolution: 1.33 Å
AuthorsAumonier, S. / Dupuy, J. / Royant, A.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-17-CE11-0013 France
Citation
Journal: Nat.Methods / Year: 2023
Title: mScarlet3: a brilliant and fast-maturing red fluorescent protein.
Authors: Gadella Jr., T.W.J. / van Weeren, L. / Stouthamer, J. / Hink, M.A. / Wolters, A.H.G. / Giepmans, B.N.G. / Aumonier, S. / Dupuy, J. / Royant, A.
#1: Journal: Nat Methods / Year: 2017
Title: mScarlet: a bright monomeric red fluorescent protein for cellular imaging.
Authors: Bindels, D.S. / Haarbosch, L. / van Weeren, L. / Postma, M. / Wiese, K.E. / Mastop, M. / Aumonier, S. / Gotthard, G. / Royant, A. / Hink, M.A. / Gadella, T.W.
History
DepositionMar 28, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 5, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Feb 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: Red fluorescent protein drFP583
B: Red fluorescent protein drFP583


Theoretical massNumber of molelcules
Total (without water)51,7302
Polymers51,7302
Non-polymers00
Water4,396244
1
A: Red fluorescent protein drFP583


Theoretical massNumber of molelcules
Total (without water)25,8651
Polymers25,8651
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Red fluorescent protein drFP583


Theoretical massNumber of molelcules
Total (without water)25,8651
Polymers25,8651
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.231, 61.862, 110.933
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 Red fluorescent protein drFP583 / DsRed


Mass: 25865.129 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Residue NRQ67 is formed by the autocatalytic cyclisation of the three consecutive amino acid residues M67, Y68 and G69
Source: (gene. exp.) Discosoma sp. (sea anemone) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9U6Y8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 244 / 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: 1.77 Å3/Da / Density % sol: 30.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M sodium chloride, 0.1 M, 0.1 M HEPES pH 7.5, 1.6 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 10, 2020
RadiationMonochromator: CHANNEL-CUT SI(111) CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.33→42.78 Å / Num. obs: 91873 / % possible obs: 97.5 % / Redundancy: 3.8 % / Biso Wilson estimate: 16.7 Å2 / CC1/2: 0.994 / Rsym value: 0.097 / Net I/σ(I): 6
Reflection shellResolution: 1.33→1.38 Å / Mean I/σ(I) obs: 0.7 / Num. unique obs: 9289 / CC1/2: 0.548 / Rsym value: 0.929 / % possible all: 99.1

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Processing

Software
NameVersionClassification
XDSdata reduction
XDSdata scaling
PHASERphasing
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LK4

5lk4


Resolution: 1.33→42.78 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.84 / SU ML: 0.07 / 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
Rfree0.2283 1157 1.3 %RANDOM
Rwork0.2001 ---
obs0.2004 90993 97.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 67.36 Å2 / Biso mean: 18.863 Å2 / Biso min: 12.02 Å2
Baniso -1Baniso -2Baniso -3
1--1.15 Å20 Å2-0 Å2
2--1.6 Å20 Å2
3----0.45 Å2
Refinement stepCycle: final / Resolution: 1.33→42.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3483 0 0 247 3730
Biso mean---27.06 -
Num. residues----430
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0133755
X-RAY DIFFRACTIONr_bond_other_d0.0010.0153478
X-RAY DIFFRACTIONr_angle_refined_deg1.8171.6745092
X-RAY DIFFRACTIONr_angle_other_deg1.4061.5998072
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5145469
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.26421.845206
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.90115654
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.7871527
X-RAY DIFFRACTIONr_chiral_restr0.0810.2461
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024273
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02889
LS refinement shellResolution: 1.33→1.362 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.389 84 -
Rwork0.406 6577 -
obs--96.19 %

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