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- PDB-5ooz: XFEL structure of the on state of a reversibly photoswitching flu... -

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Basic information

Entry
Database: PDB / ID: 5ooz
TitleXFEL structure of the on state of a reversibly photoswitching fluorescent protein determined using the grease injection method
ComponentsGreen to red photoconvertible GFP-like protein EosFP
KeywordsFLUORESCENT PROTEIN / XFEL photoswitching
Function / homologyGreen fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / generation of precursor metabolites and energy / Green to red photoconvertible GFP-like protein EosFP
Function and homology information
Biological speciesLobophyllia hemprichii (invertebrata)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsHutchison, C.D.M. / Cordon-Preciado, V. / Morgan, R.M.L. / van Thor, J.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Engineering and Physical Sciences Research Council United Kingdom
CitationJournal: Int J Mol Sci / Year: 2017
Title: X-ray Free Electron Laser Determination of Crystal Structures of Dark and Light States of a Reversibly Photoswitching Fluorescent Protein at Room Temperature.
Authors: Hutchison, C.D.M. / Cordon-Preciado, V. / Morgan, R.M.L. / Nakane, T. / Ferreira, J. / Dorlhiac, G. / Sanchez-Gonzalez, A. / Johnson, A.S. / Fitzpatrick, A. / Fare, C. / Marangos, J.P. / ...Authors: Hutchison, C.D.M. / Cordon-Preciado, V. / Morgan, R.M.L. / Nakane, T. / Ferreira, J. / Dorlhiac, G. / Sanchez-Gonzalez, A. / Johnson, A.S. / Fitzpatrick, A. / Fare, C. / Marangos, J.P. / Yoon, C.H. / Hunter, M.S. / DePonte, D.P. / Boutet, S. / Owada, S. / Tanaka, R. / Tono, K. / Iwata, S. / van Thor, J.J.
History
DepositionAug 9, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Nov 14, 2018Group: Data collection / Category: chem_comp / diffrn
Item: _chem_comp.type / _diffrn.pdbx_serial_crystal_experiment
Revision 1.3Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 2.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / pdbx_validate_polymer_linkage / pdbx_validate_rmsd_bond / pdbx_validate_torsion / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_validate_polymer_linkage.auth_atom_id_2 / _struct_conn.ptnr1_label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Green to red photoconvertible GFP-like protein EosFP


Theoretical massNumber of molelcules
Total (without water)25,7251
Polymers25,7251
Non-polymers00
Water2,918162
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.800, 74.600, 79.200
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 to red photoconvertible GFP-like protein EosFP / Skylan-NS


Mass: 25725.215 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lobophyllia hemprichii (invertebrata) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5S6Z9
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 2.24 Å3/Da / Density % sol: 45.01 %
Crystal growTemperature: 293.15 K / Method: batch mode
Details: 0.2 M lithium sulfate 0.1 M Tris-Cl pH 8.5 23-30% PEG 3350

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Data collection

DiffractionMean temperature: 293.15 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SACLA / Beamline: BL3 / Wavelength: 1.76 Å
DetectorType: MPCCD / Detector: CCD / Date: May 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.76 Å / Relative weight: 1
ReflectionResolution: 1.911→54.3 Å / Num. obs: 18901 / % possible obs: 99.74 % / Redundancy: 17.7 % / Net I/σ(I): 13.77

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.92→54.3 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.941 / SU B: 3.791 / SU ML: 0.103 / Cross valid method: THROUGHOUT / ESU R: 0.141 / ESU R Free: 0.152
RfactorNum. reflection% reflectionSelection details
Rfree0.22863 927 5.1 %RANDOM
Rwork0.15628 ---
obs0.15964 17378 97.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 35.383 Å2
Baniso -1Baniso -2Baniso -3
1-0.45 Å20 Å20 Å2
2---0.22 Å20 Å2
3----0.23 Å2
Refinement stepCycle: 1 / Resolution: 1.92→54.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1743 0 0 162 1905
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0191891
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9571.9572575
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8765249
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.58324.42195
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.83115331
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.268159
X-RAY DIFFRACTIONr_chiral_restr0.1610.2267
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211473
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.5413.141894
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.1184.6771123
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.3363.506997
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined22.73143.5232721
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.918→1.967 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree1.63 53 -
Rwork1.431 910 -
obs--69.53 %

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