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- PDB-8a6g: Room temperature rsEGFP2 with a chlorinated chromophore in the no... -

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Basic information

Entry
Database: PDB / ID: 8a6g
TitleRoom temperature rsEGFP2 with a chlorinated chromophore in the non-fluorescent OFF-state
ComponentsGreen fluorescent protein
KeywordsFLUORESCENT PROTEIN / GFP-like protein / beta-barrel / bioluminescence
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: 1.63 Å
AuthorsFadini, A. / van Thor, J.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Imperial College LondonPresident's PhD Scholarship United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/P00752X/1 United Kingdom
CitationJournal: J.Am.Chem.Soc. / Year: 2023
Title: Serial Femtosecond Crystallography Reveals that Photoactivation in a Fluorescent Protein Proceeds via the Hula Twist Mechanism.
Authors: Fadini, A. / Hutchison, C.D.M. / Morozov, D. / Chang, J. / Maghlaoui, K. / Perrett, S. / Luo, F. / Kho, J.C.X. / Romei, M.G. / Morgan, R.M.L. / Orr, C.M. / Cordon-Preciado, V. / Fujiwara, T. ...Authors: Fadini, A. / Hutchison, C.D.M. / Morozov, D. / Chang, J. / Maghlaoui, K. / Perrett, S. / Luo, F. / Kho, J.C.X. / Romei, M.G. / Morgan, R.M.L. / Orr, C.M. / Cordon-Preciado, V. / Fujiwara, T. / Nuemket, N. / Tosha, T. / Tanaka, R. / Owada, S. / Tono, K. / Iwata, S. / Boxer, S.G. / Groenhof, G. / Nango, E. / van Thor, J.J.
History
DepositionJun 17, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 19, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Feb 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


Theoretical massNumber of molelcules
Total (without water)28,5671
Polymers28,5671
Non-polymers00
Water2,234124
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.990, 62.910, 72.030
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Green fluorescent protein


Mass: 28566.648 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


Mass: 18.015 Da / Num. of mol.: 124 / 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: 39.85 %
Crystal growTemperature: 293 K / Method: microbatch
Details: 1.3M ammonium sulfate, 100mM Hepes pH 8.1, 20mM NaCl

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SACLA / Beamline: BL3 / Wavelength: 1.18 Å
DetectorType: MPCCD / Detector: CCD / Date: Jun 19, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.18 Å / Relative weight: 1
ReflectionResolution: 1.63→31.46 Å / Num. obs: 30206 / % possible obs: 100 % / Redundancy: 474 % / CC1/2: 0.99 / Net I/σ(I): 6.973
Reflection shellResolution: 1.63→1.688 Å / Num. unique obs: 2952 / CC1/2: 0.62
Serial crystallography measurementPulse photon energy: 10.5 keV / XFEL pulse repetition rate: 30 Hz
Serial crystallography sample deliveryMethod: injection
Serial crystallography sample delivery injectionCrystal conc.: 30 / Description: SACLA MICROJET / Injector diameter: 80 µm

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.27data extraction
CrystFELdata reduction
CrystFELdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6PFT

6pft


Resolution: 1.63→31.455 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.44 / Phase error: 19.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1946 1510 5.01 %
Rwork0.155 28631 -
obs0.1569 30141 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 104.08 Å2 / Biso mean: 28.5083 Å2 / Biso min: 14.15 Å2
Refinement stepCycle: final / Resolution: 1.63→31.455 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1884 0 600 125 2609
Biso mean--27.77 36.75 -
Num. residues----164
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.63-1.68260.31221330.27722566
1.6826-1.74270.29921440.2462555
1.7427-1.81250.26511360.20972579
1.8125-1.8950.24721370.16982538
1.895-1.99490.20531410.15462580
1.9949-2.11980.18971280.1562581
2.1198-2.28350.21591440.14992581
2.2835-2.51320.20241280.15462614
2.5132-2.87660.21661500.16082612
2.8766-3.62340.18621200.1412659
3.6234-31.4550.15131490.1392766

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