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- PDB-9j0q: Structure of mEos3.2 in the green fluorescent state -

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Basic information

Entry
Database: PDB / ID: 9j0q
TitleStructure of mEos3.2 in the green fluorescent state
ComponentsGreen to red photoconvertible GFP-like protein EosFP
KeywordsFLUORESCENT PROTEIN / Green-to-red / photoconvertible / fluorescent proteins
Function / homologyGreen fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / generation of precursor metabolites and energy / Green to red photoconvertible GFP-like protein EosFP
Function and homology information
Biological speciesLobophyllia hemprichii (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.34 Å
AuthorsZheng, S.P. / Shi, X.R.
Funding support1items
OrganizationGrant numberCountry
Other government
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2025
Title: Structural basis for the fast maturation of pcStar, a photoconvertible fluorescent protein.
Authors: Zheng, S. / Shi, X. / Lin, J. / Yang, Y. / Xin, Y. / Bai, X. / Zhu, H. / Chen, H. / Wu, J. / Zheng, X. / Lin, L. / Huang, Z. / Yang, S. / Hu, F. / Liu, W.
History
DepositionAug 2, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 16, 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)28,7343
Polymers28,5421
Non-polymers1922
Water4,414245
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)38.675, 70.683, 91.129
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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


Mass: 28542.238 Da / Num. of mol.: 1 / Mutation: N11K,E70K,H74N,I102N,H121Y,V123T,T158E,Y189A
Source method: isolated from a genetically manipulated source
Details: MGSSHHHHHHSQDPLEVLFQGPEFMSAIKPDMKIKLRMEGNVNGHHFVIDGDGTGKPFEGKQSMDLEVKEGGPLPFAFDILTTAF(5SQ) ...Details: MGSSHHHHHHSQDPLEVLFQGPEFMSAIKPDMKIKLRMEGNVNGHHFVIDGDGTGKPFEGKQSMDLEVKEGGPLPFAFDILTTAF(5SQ)NRVFAKYPDNIQDYFKQSFPKGYSWERSLTFEDGGICNARNDITMEGDTFYNKVRFYGTNFPANGPVMQKKTLKWEPSTEKMYVRDGVLTGDIEMALLLEGNAHYRCDFRTTYKAKEKGVKLPGAHFVDHCIEILSHDKDYNKVKLYEHAVAHSG(SO4)LPDNARR
Source: (gene. exp.) Lobophyllia hemprichii (invertebrata) / Production host: Escherichia coli (E. coli) / References: UniProt: Q5S6Z9
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 245 / 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: 2.18 Å3/Da / Density % sol: 43.63 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Lithium sulfate, 0.1 M MES 6.0, 20 % w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 4, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.34→55.85 Å / Num. obs: 56619 / % possible obs: 100 % / Redundancy: 12.7 % / Biso Wilson estimate: 11.65 Å2 / CC1/2: 0.999 / Net I/σ(I): 15.81
Reflection shellResolution: 1.34→1.42 Å / Num. unique obs: 8150 / CC1/2: 0.9

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5OOZ

5ooz


Resolution: 1.34→25.08 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 0.02 / Phase error: 13.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.166 1919 3.55 %
Rwork0.1447 --
obs0.1455 54091 95.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.34→25.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1779 0 5 245 2029
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061837
X-RAY DIFFRACTIONf_angle_d1.4362476
X-RAY DIFFRACTIONf_dihedral_angle_d9.68242
X-RAY DIFFRACTIONf_chiral_restr0.09248
X-RAY DIFFRACTIONf_plane_restr0.009320
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.34-1.380.16121220.15593309X-RAY DIFFRACTION86
1.38-1.410.17781260.14193465X-RAY DIFFRACTION90
1.41-1.460.16561310.14723504X-RAY DIFFRACTION92
1.46-1.50.19271310.14443582X-RAY DIFFRACTION92
1.5-1.560.17771330.12833611X-RAY DIFFRACTION94
1.56-1.620.1521380.12113710X-RAY DIFFRACTION96
1.62-1.690.14061360.1233708X-RAY DIFFRACTION96
1.69-1.780.16061370.1213758X-RAY DIFFRACTION97
1.78-1.890.1621400.1253794X-RAY DIFFRACTION98
1.89-2.040.13491430.11893851X-RAY DIFFRACTION99
2.04-2.240.14261420.12883883X-RAY DIFFRACTION99
2.24-2.570.18341440.15023907X-RAY DIFFRACTION99
2.57-3.230.14771460.1593957X-RAY DIFFRACTION100
3.24-25.080.19431500.16714133X-RAY DIFFRACTION100

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