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- PDB-8aha: rsEGFP2 photoswitched to its off-state at 100K -

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Basic information

Entry
Database: PDB / ID: 8aha
TitlersEGFP2 photoswitched to its off-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: 2.38 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

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Assembly

Deposited unit
A: Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3019
Polymers28,5321
Non-polymers7698
Water1,11762
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2220 Å2
ΔGint-123 kcal/mol
Surface area11030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.400, 60.755, 71.580
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.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 1.99 Å3/Da / Density % sol: 38.31 %
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: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Feb 3, 2021
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.38→46.32 Å / Num. obs: 124380 / % possible obs: 99.88 % / Redundancy: 13 % / Biso Wilson estimate: 33.79 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rpim(I) all: 0.07113 / Net I/σ(I): 11.44
Reflection shellResolution: 2.38→2.465 Å / Redundancy: 13.5 % / Mean I/σ(I) obs: 2.23 / Num. unique obs: 12739 / CC1/2: 0.714 / CC star: 0.913 / Rpim(I) all: 0.4082 / % possible all: 100

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Processing

Software
NameVersionClassification
MxCuBE3data collection
autoPROC1.1.7data reduction
Coot0.9.6model building
MOLREP11.7.03phasing
REFMAC5.8.0267refinement
PHENIX1.20.1_4487refinement
autoPROC1.1.7data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DTX

5dtx


Resolution: 2.38→46.32 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.9299
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2234 493 5.12 %
Rwork0.1862 9145 -
obs0.1882 9638 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.21 Å2
Refinement stepCycle: LAST / Resolution: 2.38→46.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1905 0 40 62 2007
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00771984
X-RAY DIFFRACTIONf_angle_d0.99942687
X-RAY DIFFRACTIONf_chiral_restr0.059284
X-RAY DIFFRACTIONf_plane_restr0.0066342
X-RAY DIFFRACTIONf_dihedral_angle_d13.9249717
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.38-2.620.30481170.1862239X-RAY DIFFRACTION100
2.62-2.990.25841290.19752230X-RAY DIFFRACTION99.7
2.99-3.770.22721200.17232288X-RAY DIFFRACTION100
3.77-46.320.18961270.19122388X-RAY DIFFRACTION99.8

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