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- PDB-8a7v: Room temperature rsEGFP2 in its OFF-state obtained with SFX -

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Basic information

Entry
Database: PDB / ID: 8a7v
TitleRoom temperature rsEGFP2 in its OFF-state obtained with SFX
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: 1.46 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 21, 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)28,5321
Polymers28,5321
Non-polymers00
Water3,117173
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.970, 63.040, 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: 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


Mass: 18.015 Da / Num. of mol.: 173 / 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: 2.07 Å3/Da / Density % sol: 40.51 %
Crystal growTemperature: 293 K / Method: microbatch
Details: 120 mM HEPES pH 8.0, 1.5 M ammonium sulphate, 20 mM 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: Nov 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.18 Å / Relative weight: 1
ReflectionResolution: 1.46→47.44 Å / Num. obs: 36821 / % possible obs: 88.77 % / Redundancy: 191.82 % / CC1/2: 0.98 / Net I/σ(I): 7.537
Reflection shellResolution: 1.463→1.514 Å / Num. unique obs: 340 / CC1/2: 0.7
Serial crystallography sample deliveryMethod: injection

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
PDB_EXTRACT3.27data extraction
CrystFELdata reduction
CrystFELdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6T39

6t39


Resolution: 1.46→47.44 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.492 / SU ML: 0.053 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.075 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1952 1790 4.9 %RANDOM
Rwork0.1696 ---
obs0.1709 35031 88.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 142.39 Å2 / Biso mean: 27.071 Å2 / Biso min: 12.52 Å2
Baniso -1Baniso -2Baniso -3
1--0.84 Å2-0 Å2-0 Å2
2--0.27 Å2-0 Å2
3---0.56 Å2
Refinement stepCycle: final / Resolution: 1.46→47.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1883 0 536 173 2592
Biso mean--27.08 40.43 -
Num. residues----164
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0191985
X-RAY DIFFRACTIONr_bond_other_d0.0020.021776
X-RAY DIFFRACTIONr_angle_refined_deg2.2811.9672689
X-RAY DIFFRACTIONr_angle_other_deg1.17934149
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5345239
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.09324.89696
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.59615336
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.657156
X-RAY DIFFRACTIONr_chiral_restr0.1410.2286
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0212195
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02396
LS refinement shellResolution: 1.462→1.5 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.608 5 -
Rwork0.511 101 -
all-106 -
obs--3.48 %

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