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- PDB-5lk4: Structure of the Red Fluorescent Protein mScarlet at pH 7.8 -

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Basic information

Entry
Database: PDB / ID: 5lk4
TitleStructure of the Red Fluorescent Protein mScarlet at pH 7.8
ComponentsmScarlet
KeywordsFLUORESCENT PROTEIN / beta barrel / red fluorescent protein
Function / homology
Function and homology information


bioluminescence / generation of precursor metabolites and energy
Similarity search - Function
Green Fluorescent Protein / Green fluorescent protein / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / PHOSPHATE ION / Red fluorescent protein drFP583
Similarity search - Component
Biological speciesDiscosoma sp. (sea anemone)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.47 Å
AuthorsAumonier, S. / Gotthard, G. / Royant, A.
CitationJournal: 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
DepositionJul 20, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 7, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2017Group: Database references
Revision 2.0Sep 14, 2022Group: Database references / Non-polymer description / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / entity_name_com / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _chem_comp.formula / _chem_comp.formula_weight ..._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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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.seq_align_beg / _struct_ref_seq.seq_align_end
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

Downloads & links

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Assembly

Deposited unit
A: mScarlet
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8938
Polymers24,8971
Non-polymers9967
Water3,531196
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2950 Å2
ΔGint18 kcal/mol
Surface area9930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.200, 35.640, 86.010
Angle α, β, γ (deg.)90.000, 109.690, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-461-

HOH

21A-592-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein mScarlet / DsRed


Mass: 24897.078 Da / Num. of mol.: 1 / Fragment: Red Fluorescent Protein mScarlet
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Discosoma sp. (sea anemone) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9U6Y8

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Non-polymers , 5 types, 203 molecules

#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 196 / 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: 2.44 Å3/Da / Density % sol: 49.59 %
Description: mScarlet crystal was soaked 45 min in 40% PEG 300, 100mM Sodium Phosphate Citrate pH 7.8
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.2 / Details: 35-45% PEG 300, 100mM Sodium Phosphate Citrate / PH range: 4.0 - 5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 18, 2015
RadiationMonochromator: Si [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.47→81 Å / Num. obs: 40759 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Biso Wilson estimate: 20.552 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.065 / Net I/σ(I): 10.99
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
1.47-1.510.5412.040.604198.1
1.51-1.550.4672.450.702197.5
1.55-1.590.4022.860.759197.3
1.59-1.640.3333.430.838197.7
1.64-1.70.294.060.881198.8
1.7-1.760.2235.030.933198.9
1.76-1.820.1686.190.958199
1.82-1.90.1387.410.97198.5
1.9-1.980.1059.530.982199.2
1.98-2.080.08212.130.991199.4
2.08-2.190.0713.330.993199.2
2.19-2.320.06414.690.994199.8
2.32-2.480.05615.950.994198.3
2.48-2.680.05118.170.996199.4
2.68-2.940.0421.720.997199.9
2.94-3.290.03824.980.997198.9
3.29-3.80.03429.130.998198.6
3.8-4.650.03434.210.997198.3
4.65-6.570.03431.780.998198.2
6.570.03931.860.997196.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
REFMAC5.8.0135refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdbid 3KCS

3kcs


Resolution: 1.47→80.98 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.967 / SU B: 2.397 / SU ML: 0.039 / Cross valid method: FREE R-VALUE / σ(F): 0 / ESU R: 0.068 / ESU R Free: 0.059 / Details: REFMAC 5.8
RfactorNum. reflection% reflectionSelection details
Rfree0.1669 2008 4.9 %RANDOM
Rwork0.1368 ---
obs0.1382 38751 98.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 76.5 Å2 / Biso mean: 16.993 Å2 / Biso min: 8.79 Å2
Baniso -1Baniso -2Baniso -3
1--0.42 Å20 Å20.02 Å2
2--0.22 Å20 Å2
3---0.15 Å2
Refinement stepCycle: final / Resolution: 1.47→80.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1739 0 65 198 2002
Biso mean--33.28 31.86 -
Num. residues----217
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0191993
X-RAY DIFFRACTIONr_bond_other_d0.0020.021916
X-RAY DIFFRACTIONr_angle_refined_deg1.6431.9952690
X-RAY DIFFRACTIONr_angle_other_deg0.89734465
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4925259
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.09723.66790
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.54715357
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2851514
X-RAY DIFFRACTIONr_chiral_restr0.0870.2273
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212199
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02449
X-RAY DIFFRACTIONr_mcbond_it1.0331.299913
X-RAY DIFFRACTIONr_mcbond_other1.021.295912
X-RAY DIFFRACTIONr_mcangle_it1.1881.9491150
X-RAY DIFFRACTIONr_rigid_bond_restr1.48133908
X-RAY DIFFRACTIONr_sphericity_free27.139573
X-RAY DIFFRACTIONr_sphericity_bonded5.33353970
LS refinement shellResolution: 1.47→1.508 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 142 -
Rwork0.28 2835 -
all-2977 -
obs--98.12 %

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