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- PDB-5o89: Crystal Structure of rsEGFP2 in the fluorescent on-state determin... -

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Entry
Database: PDB / ID: 5o89
TitleCrystal Structure of rsEGFP2 in the fluorescent on-state determined by SFX
ComponentsGreen fluorescent protein
KeywordsFLUORESCENT PROTEIN / photoswitching on state fluorescent state chromophore SFX serial femtosecond crystallography CXI LCLS time resolved crystallography chromohore isomerisation
Function / homology
Function and homology information


bioluminescence / generation of precursor metabolites and energy
Similarity search - Function
Green Fluorescent Protein / Green fluorescent protein / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Green fluorescent protein
Similarity search - Component
Biological speciesAequorea victoria (jellyfish)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsCoquelle, N. / Sliwa, M. / Woodhouse, J. / Schiro, G. / Adam, V. / Aquila, A. / Barends, T.R.M. / Boutet, S. / Byrdin, M. / Carbajo, S. ...Coquelle, N. / Sliwa, M. / Woodhouse, J. / Schiro, G. / Adam, V. / Aquila, A. / Barends, T.R.M. / Boutet, S. / Byrdin, M. / Carbajo, S. / De la Mora, E. / Doak, R.B. / Feliks, M. / Fieschi, F. / Foucar, L. / Guillon, V. / Hilpert, M. / Hunter, M. / Jakobs, S. / Koglin, J.E. / Kovacsova, G. / Lane, T.J. / Levy, B. / Liang, M. / Nass, K. / Ridard, J. / Robinson, J.S. / Roome, C.M. / Ruckebusch, C. / Seaberg, M. / Thepaut, M. / Cammarata, M. / Demachy, I. / Field, M. / Shoeman, R.L. / Bourgeois, D. / Colletier, J.P. / Schlichting, I. / Weik, M.
CitationJournal: Nat Chem / Year: 2018
Title: Chromophore twisting in the excited state of a photoswitchable fluorescent protein captured by time-resolved serial femtosecond crystallography.
Authors: Coquelle, N. / Sliwa, M. / Woodhouse, J. / Schiro, G. / Adam, V. / Aquila, A. / Barends, T.R.M. / Boutet, S. / Byrdin, M. / Carbajo, S. / De la Mora, E. / Doak, R.B. / Feliks, M. / Fieschi, ...Authors: Coquelle, N. / Sliwa, M. / Woodhouse, J. / Schiro, G. / Adam, V. / Aquila, A. / Barends, T.R.M. / Boutet, S. / Byrdin, M. / Carbajo, S. / De la Mora, E. / Doak, R.B. / Feliks, M. / Fieschi, F. / Foucar, L. / Guillon, V. / Hilpert, M. / Hunter, M.S. / Jakobs, S. / Koglin, J.E. / Kovacsova, G. / Lane, T.J. / Levy, B. / Liang, M. / Nass, K. / Ridard, J. / Robinson, J.S. / Roome, C.M. / Ruckebusch, C. / Seaberg, M. / Thepaut, M. / Cammarata, M. / Demachy, I. / Field, M. / Shoeman, R.L. / Bourgeois, D. / Colletier, J.P. / Schlichting, I. / Weik, M.
History
DepositionJun 12, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 13, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Nov 14, 2018Group: Data collection / Category: diffrn / Item: _diffrn.pdbx_serial_crystal_experiment
Revision 1.3Dec 13, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_related_exp_data_set / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Jan 17, 2024Group: Refinement description / Category: 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)28,1001
Polymers28,1001
Non-polymers00
Water5,567309
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area640 Å2
ΔGint-2 kcal/mol
Surface area11690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.670, 62.260, 71.880
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Green fluorescent protein / / rsEGFP2


Mass: 28099.686 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 (E. coli) / References: UniProt: P42212
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 309 / Source method: isolated from a natural source / Formula: H2O

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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: 2.06 Å3/Da / Density % sol: 40.21 %
Crystal growTemperature: 293 K / Method: batch mode / pH: 8 / Details: 2 M ammonium sulphate, 20 mM NaCl, 120 mM HEPES

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: CXI / Wavelength: 1.3 / Wavelength: 1.3 Å
DetectorType: CS-PAD CXI-1 / Detector: PIXEL / Date: May 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 26122 / % possible obs: 99.8 % / Redundancy: 254 % / R split: 0.091 / Net I/σ(I): 9.2
Reflection shellResolution: 1.7→1.76 Å / R split: 0.591

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Processing

Software
NameVersionClassification
PHENIX(1.10_2152: ???)refinement
CrystFEL0.6.1data reduction
CrystFEL0.6.1data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DTX

5dtx


Resolution: 1.7→21.737 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1948 1304 4.99 %
Rwork0.1675 --
obs0.1689 26122 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→21.737 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1960 0 0 309 2269
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062009
X-RAY DIFFRACTIONf_angle_d0.9732712
X-RAY DIFFRACTIONf_dihedral_angle_d14.4071185
X-RAY DIFFRACTIONf_chiral_restr0.061290
X-RAY DIFFRACTIONf_plane_restr0.005352
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.7680.29671390.24012677X-RAY DIFFRACTION99
1.768-1.84850.24061450.19042733X-RAY DIFFRACTION100
1.8485-1.94590.2091420.15842726X-RAY DIFFRACTION100
1.9459-2.06770.18831430.14912731X-RAY DIFFRACTION100
2.0677-2.22720.20581440.15082718X-RAY DIFFRACTION100
2.2272-2.4510.20581450.16672750X-RAY DIFFRACTION100
2.451-2.80510.20731430.17682762X-RAY DIFFRACTION100
2.8051-3.53170.18841490.16582794X-RAY DIFFRACTION100
3.5317-21.73850.16961540.16472927X-RAY DIFFRACTION100

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