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- PDB-9gvr: mEos4b-L93M photoconvertible fluorescent protein -

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Basic information

Entry
Database: PDB / ID: 9gvr
TitlemEos4b-L93M photoconvertible fluorescent protein
ComponentsGreen to red photoconvertible GFP-like protein EosFP
KeywordsFLUORESCENT PROTEIN / beta-barrel / luminescent protein
Function / homologyGreen fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / generation of precursor metabolites and energy / DI(HYDROXYETHYL)ETHER / Green to red photoconvertible GFP-like protein EosFP
Function and homology information
Biological speciesLobophyllia hemprichii (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsAdam, V.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-20-CE11-0013-01 France
CitationJournal: Protein Sci. / Year: 2025
Title: Decoding mEos4b day-long maturation and engineering fast-maturing variants.
Authors: Maity, A. / Glushonkov, O. / Ayala, I. / Tacnet, P. / Wulffele, J. / Frachet, P. / Brutscher, B. / Bourgeois, D. / Adam, V.
History
DepositionSep 25, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 30, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Green to red photoconvertible GFP-like protein EosFP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4925
Polymers25,0811
Non-polymers4104
Water4,324240
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.278, 57.300, 102.755
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Green to red photoconvertible GFP-like protein EosFP


Mass: 25081.438 Da / Num. of mol.: 1 / Mutation: L93M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lobophyllia hemprichii (invertebrata) / Production host: Escherichia coli (E. coli) / References: UniProt: Q5S6Z9
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 240 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.31 Å3/Da / Density % sol: 46.64 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1 M HEPES pH 8.5, 32 % PEG 1000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Feb 9, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.86→50.04 Å / Num. obs: 20037 / % possible obs: 99.7 % / Redundancy: 8.4 % / Biso Wilson estimate: 11.59 Å2 / CC1/2: 0.993 / CC star: 0.998 / Rpim(I) all: 0.08116 / Rrim(I) all: 0.2372 / Net I/σ(I): 8.92
Reflection shellResolution: 1.86→1.93 Å / Redundancy: 8.8 % / Mean I/σ(I) obs: 2.46 / Num. unique obs: 1913 / CC1/2: 0.718 / CC star: 0.914 / Rpim(I) all: 0.442 / % possible all: 97.8

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.86→38.25 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2071 2000 10 %
Rwork0.1678 --
obs0.1718 19992 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.86→38.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1785 0 0 240 2025
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041914
X-RAY DIFFRACTIONf_angle_d0.7742588
X-RAY DIFFRACTIONf_dihedral_angle_d11.338273
X-RAY DIFFRACTIONf_chiral_restr0.053259
X-RAY DIFFRACTIONf_plane_restr0.005339
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.86-1.910.31851370.2241229X-RAY DIFFRACTION97
1.91-1.960.27491410.19911270X-RAY DIFFRACTION99
1.96-2.020.24221360.19631229X-RAY DIFFRACTION100
2.02-2.080.25571430.18461286X-RAY DIFFRACTION100
2.08-2.160.25031400.18181259X-RAY DIFFRACTION100
2.16-2.250.20691420.16521269X-RAY DIFFRACTION100
2.25-2.350.19581410.17471274X-RAY DIFFRACTION100
2.35-2.470.2171430.17531286X-RAY DIFFRACTION100
2.47-2.630.20931420.1711285X-RAY DIFFRACTION100
2.63-2.830.19761420.16261274X-RAY DIFFRACTION100
2.83-3.110.17951430.16291288X-RAY DIFFRACTION100
3.11-3.560.1951470.15081318X-RAY DIFFRACTION100
3.56-4.490.1541460.13221316X-RAY DIFFRACTION100
4.49-38.250.19851570.17381409X-RAY DIFFRACTION100

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