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- PDB-6t39: Crystal structure of rsEGFP2 in its off-state determined by SFX -

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Basic information

Entry
Database: PDB / ID: 6t39
TitleCrystal structure of rsEGFP2 in its off-state determined by SFX
ComponentsGreen fluorescent protein
KeywordsFLUORESCENT PROTEIN / rsEGFP2 / Green Fluorescent Protein / RSFP
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 / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsWoodhouse, J. / Coquelle, N. / Adam, V. / Barends, T.R.M. / De La Mora, E. / Bourgeois, D. / Colletier, J.P. / Schlichting, I. / Weik, M.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-15-CE32-0004 France
CitationJournal: Nat Commun / Year: 2020
Title: Photoswitching mechanism of a fluorescent protein revealed by time-resolved crystallography and transient absorption spectroscopy.
Authors: Woodhouse, J. / Nass Kovacs, G. / Coquelle, N. / Uriarte, L.M. / Adam, V. / Barends, T.R.M. / Byrdin, M. / de la Mora, E. / Bruce Doak, R. / Feliks, M. / Field, M. / Fieschi, F. / Guillon, V. ...Authors: Woodhouse, J. / Nass Kovacs, G. / Coquelle, N. / Uriarte, L.M. / Adam, V. / Barends, T.R.M. / Byrdin, M. / de la Mora, E. / Bruce Doak, R. / Feliks, M. / Field, M. / Fieschi, F. / Guillon, V. / Jakobs, S. / Joti, Y. / Macheboeuf, P. / Motomura, K. / Nass, K. / Owada, S. / Roome, C.M. / Ruckebusch, C. / Schiro, G. / Shoeman, R.L. / Thepaut, M. / Togashi, T. / Tono, K. / Yabashi, M. / Cammarata, M. / Foucar, L. / Bourgeois, D. / Sliwa, M. / Colletier, J.P. / Schlichting, I. / Weik, M.
History
DepositionOct 10, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 19, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)28,5321
Polymers28,5321
Non-polymers00
Water4,450247
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area640 Å2
ΔGint-2 kcal/mol
Surface area11000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.680, 62.890, 71.710
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 247 / 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: 2.04 Å3/Da / Density % sol: 39.67 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 8 / Details: 100 mM HEPES pH 8.0, 2.5 M ammonium sulphate

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SACLA / Beamline: BL3 / Wavelength: 1.24 Å
DetectorType: MPCCD / Detector: CCD / Date: Jul 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.24 Å / Relative weight: 1
ReflectionResolution: 1.6→29.46 Å / Num. obs: 31252 / % possible obs: 99.87 % / Redundancy: 235 % / R split: 0.1164 / Net I/σ(I): 6.8
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 5 % / Num. unique obs: 1832 / R split: 0.6948 / % possible all: 88.25
Serial crystallography measurementFocal spot size: 2.24 µm2 / Pulse duration: 10 fsec. / Pulse energy: 300 µJ / Pulse photon energy: 10 keV / XFEL pulse repetition rate: 30 Hz
Serial crystallography sample deliveryMethod: injection

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Processing

Software
NameVersionClassification
PHENIX1.14refinement
CrystFEL0.6.2data reduction
CrystFEL0.6.2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DTY

5dty


Resolution: 1.6→29.46 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2024 --
Rwork0.1653 --
obs-31252 99.87 %
Displacement parametersBiso mean: 20.24 Å2
Refinement stepCycle: LAST / Resolution: 1.6→29.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1896 0 0 247 2143
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01752424
X-RAY DIFFRACTIONf_angle_d1.46453338
X-RAY DIFFRACTIONf_chiral_restr0.2903353
X-RAY DIFFRACTIONf_plane_restr0.0083448
X-RAY DIFFRACTIONf_dihedral_angle_d20.1648908

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