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- PDB-5oq9: XFEL structure of the off state of a reversibly photoswitching fl... -

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Basic information

Entry
Database: PDB / ID: 5oq9
TitleXFEL structure of the off state of a reversibly photoswitching fluorescent protein determined using the droplet on demand 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: 1.51 Å
AuthorsHutchison, C.D.M. / Cordon-Preciado, V. / Morgan, R.M.L. / van Thor, J.J.
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 11, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2018Group: Data collection / Category: chem_comp / diffrn
Item: _chem_comp.type / _diffrn.pdbx_serial_crystal_experiment
Revision 1.2Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...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_validate_rmsd_bond / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_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)25,7241
Polymers25,7241
Non-polymers00
Water3,729207
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10030 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


Mass: 25724.270 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


Mass: 18.015 Da / Num. of mol.: 207 / 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: 2.31 Å3/Da / Density % sol: 46.83 %
Crystal growTemperature: 293 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 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SACLA / Beamline: BL3 / Wavelength: 1.18 Å
DetectorType: MPCCD / Detector: CCD / Date: Jul 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.18 Å / Relative weight: 1
ReflectionResolution: 1.45→54.3 Å / Num. obs: 37792 / % possible obs: 90.4 % / Redundancy: 11.9 % / Net I/σ(I): 6.84

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.51→54.3 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.877 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.092 / ESU R Free: 0.104
RfactorNum. reflection% reflectionSelection details
Rfree0.234 1471 5 %RANDOM
Rwork0.175 ---
obs0.178 28125 78.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 30.11 Å2
Baniso -1Baniso -2Baniso -3
1-0.82 Å20 Å20 Å2
2---0.36 Å20 Å2
3----0.46 Å2
Refinement stepCycle: LAST / Resolution: 1.51→54.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1736 0 0 207 1943
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.021838
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.181.9652490
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8635229
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.25424.09188
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.44715318
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.79158
X-RAY DIFFRACTIONr_chiral_restr0.1430.2255
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0211422
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
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: 1.51→1.55 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.705 1 -
Rwork0.735 44 -
obs--1.65 %

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