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- PDB-8ahb: rsEGFP2 photoswitched to its off-state at room temperature and ba... -

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Basic information

Entry
Database: PDB / ID: 8ahb
TitlersEGFP2 photoswitched to its off-state at room temperature and back-switched to its on-state at 100K
ComponentsGreen fluorescent protein
KeywordsFLUORESCENT PROTEIN / RSFP / Switchable / PTFP / rsEGFP2
Function / homologyGreen fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / generation of precursor metabolites and energy / Green fluorescent protein
Function and homology information
Biological speciesAequorea victoria (jellyfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsMantovanelli, A. / Adam, V.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-17-CE11-0047-01 France
CitationJournal: J.Am.Chem.Soc. / Year: 2023
Title: Photophysical Studies at Cryogenic Temperature Reveal a Novel Photoswitching Mechanism of rsEGFP2.
Authors: Mantovanelli, A.M.R. / Glushonkov, O. / Adam, V. / Wulffele, J. / Thedie, D. / Byrdin, M. / Gregor, I. / Nevskyi, O. / Enderlein, J. / Bourgeois, D.
History
DepositionJul 21, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 19, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 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

Downloads & links

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Assembly

Deposited unit
A: Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9165
Polymers28,5321
Non-polymers3844
Water1,58588
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1410 Å2
ΔGint-60 kcal/mol
Surface area10950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.668, 61.759, 70.445
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
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 fluorescent protein


Mass: 28532.203 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P42212
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 1.97 Å3/Da / Density % sol: 37.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.1 / Details: 100 mM HEPES buffer, pH 8.1 1.9 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: 0.9763 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 18, 2022
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.79→46.44 Å / Num. obs: 254080 / % possible obs: 99.36 % / Redundancy: 11.8 % / Biso Wilson estimate: 34.59 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.1268 / Rpim(I) all: 0.03823 / Net I/σ(I): 10.87
Reflection shellResolution: 1.79→1.858 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 0.45 / Num. unique obs: 14673 / CC1/2: 0.237 / CC star: 0.619 / % possible all: 94.43

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Processing

Software
NameVersionClassification
MxCuBE3data collection
XDSdata reduction
Coot0.9.6model building
MOLREP11.7.03phasing
REFMAC5.8.0267refinement
PHENIX1.20.1_4487refinement
XSCALEdata scaling
pointlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DTY

5dty


Resolution: 1.79→46.44 Å / SU ML: 0.3616 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.8556
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2196 2014 4.98 %
Rwork0.192 38431 -
obs0.1934 40445 99.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.37 Å2
Refinement stepCycle: LAST / Resolution: 1.79→46.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1885 0 20 88 1993
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061987
X-RAY DIFFRACTIONf_angle_d0.91942695
X-RAY DIFFRACTIONf_chiral_restr0.0574286
X-RAY DIFFRACTIONf_plane_restr0.0062349
X-RAY DIFFRACTIONf_dihedral_angle_d13.4181727
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.79-1.840.47751310.49392496X-RAY DIFFRACTION90.27
1.84-1.890.40351420.42692749X-RAY DIFFRACTION99.79
1.89-1.940.34471440.36242801X-RAY DIFFRACTION99.73
1.94-2.010.31771450.27982762X-RAY DIFFRACTION99.9
2.01-2.080.30581420.25592769X-RAY DIFFRACTION99.73
2.08-2.160.27281430.23232748X-RAY DIFFRACTION99.86
2.16-2.260.26441440.21062767X-RAY DIFFRACTION99.86
2.26-2.380.22791450.20462763X-RAY DIFFRACTION99.93
2.38-2.530.26881430.18362757X-RAY DIFFRACTION99.9
2.53-2.720.27731470.19262770X-RAY DIFFRACTION100
2.72-30.22541470.19252742X-RAY DIFFRACTION99.93
3-3.430.18981480.16832786X-RAY DIFFRACTION99.9
3.43-4.320.17061470.1522759X-RAY DIFFRACTION99.93
4.33-46.440.17451460.16482762X-RAY DIFFRACTION99.97

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