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- PDB-6goy: Structure of mEos4b in the green fluorescent state -

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Basic information

Entry
Database: PDB / ID: 6goy
TitleStructure of mEos4b in the green fluorescent state
ComponentsGreen to red photoconvertible GFP-like protein EosFP
KeywordsFLUORESCENT PROTEIN
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
DI(HYDROXYETHYL)ETHER / Green to red photoconvertible GFP-like protein EosFP
Similarity search - Component
Biological speciesLobophyllia hemprichii (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsDe Zitter, E. / Adam, V. / Byrdin, M. / Van Meervelt, L. / Dedecker, P. / Bourgeois, D.
Funding support Belgium, France, 4items
OrganizationGrant numberCountry
Research Foundation - Flanders Belgium
Grenoble Instruct-ERIC Center (ISBG)UMS 3518 CNRS-CEA-UGA-EMBL France
FRISBIANR-10-INBS-05-02 France
GRALANR-10-LABX-49-01 France
CitationJournal: Nat.Methods / Year: 2019
Title: Mechanistic investigation of mEos4b reveals a strategy to reduce track interruptions in sptPALM.
Authors: De Zitter, E. / Thedie, D. / Monkemoller, V. / Hugelier, S. / Beaudouin, J. / Adam, V. / Byrdin, M. / Van Meervelt, L. / Dedecker, P. / Bourgeois, D.
History
DepositionJun 4, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 22, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Aug 7, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Sep 1, 2021Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Database references / Derived calculations / Non-polymer description / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_2 / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_entity_instance_feature / pdbx_poly_seq_scheme / pdbx_struct_mod_residue / struct_conn / struct_ref_seq_dif
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity_poly.pdbx_seq_one_letter_code / _entity_poly_seq.mon_id / _entity_src_gen.gene_src_common_name / _pdbx_entity_instance_feature.auth_comp_id / _pdbx_entity_instance_feature.comp_id / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_ref_seq_dif.mon_id / _struct_ref_seq_dif.pdbx_seq_db_seq_num
Revision 3.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_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 / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id
Revision 3.1Jan 17, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 3.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)29,9335
Polymers29,5661
Non-polymers3664
Water4,846269
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area980 Å2
ΔGint9 kcal/mol
Surface area10160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.600, 58.090, 103.270
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 to red photoconvertible GFP-like protein EosFP


Mass: 29566.309 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lobophyllia hemprichii (invertebrata) / Plasmid: pRSETb / Production host: Escherichia coli (E. coli) / Variant (production host): JM109(DE3) / References: UniProt: Q5S6Z9
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 269 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.96 Å3/Da / Density % sol: 37.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 100 mM HEPES, 30 % PEG 1000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 25, 2017
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→38.593 Å / Num. obs: 27933 / % possible obs: 97.2 % / Redundancy: 2.753 % / Biso Wilson estimate: 16.87 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.1 / Rrim(I) all: 0.121 / Χ2: 0.991 / Net I/σ(I): 6.59
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.65-1.692.7410.5071.8220830.6990.62599
1.69-1.742.6870.4312.1219970.7740.53398.4
1.74-1.792.6210.3582.4919130.8010.44396.7
1.79-1.842.820.3023.0919320.8750.37199.4
1.84-1.912.8020.2393.8218490.9090.29499.7
1.91-1.972.7520.2064.4118000.9320.25399.2
1.97-2.052.7270.1665.2617460.9530.20498.7
2.05-2.132.6150.1465.9115880.9620.17995.3
2.13-2.222.8120.1356.9215980.9660.16498.4
2.22-2.332.8040.1187.3715320.9810.14398.8
2.33-2.462.8190.1118.2814480.9720.13697.9
2.46-2.612.7710.0988.9613760.9790.11997.7
2.61-2.792.6340.0899.4412640.980.10894.6
2.79-3.012.8890.08411.0612030.9820.10197.4
3.01-3.32.8470.07711.7711050.9850.09396.2
3.3-3.692.7820.07612.899910.9830.09294.2
3.69-4.262.6980.07113.348480.9850.08691.4
4.26-5.222.8460.06114.127490.9910.07394.1
5.22-7.382.7560.06513.345830.9870.07990.5
7.38-38.5932.7620.06613.83280.9870.0885.9

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Processing

Software
NameVersionClassification
XDSVERSION Jun 1, 2017data reduction
XSCALEVERSION Jun 1, 2017data scaling
PHENIX1.11refinement
PDB_EXTRACT3.24data extraction
PHASER2.7.16phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZUX

1zux


Resolution: 1.65→38.593 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 19.06
RfactorNum. reflection% reflection
Rfree0.2039 1396 5 %
Rwork0.1675 --
obs0.1693 27927 97.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 66.77 Å2 / Biso mean: 19.4289 Å2 / Biso min: 7.77 Å2
Refinement stepCycle: final / Resolution: 1.65→38.593 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1774 0 24 269 2067
Biso mean--38.21 30.52 -
Num. residues----221
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041983
X-RAY DIFFRACTIONf_angle_d0.7862693
X-RAY DIFFRACTIONf_chiral_restr0.053268
X-RAY DIFFRACTIONf_plane_restr0.004362
X-RAY DIFFRACTIONf_dihedral_angle_d9.9811564
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6498-1.70880.26021390.24852651279098
1.7088-1.77720.29251370.22732608274597
1.7772-1.85810.26291410.20522666280799
1.8581-1.95610.23551400.18692671281199
1.9561-2.07860.2361410.17842680282199
2.0786-2.23910.22691380.16822622276097
2.2391-2.46440.2371400.16662660280098
2.4644-2.82090.21241390.16472642278196
2.8209-3.55360.1731400.15122669280996
3.5536-38.60320.15491410.14492662280391

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