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- PDB-6gp1: Structure of mEos4b in the red long-lived dark state -

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Basic information

Entry
Database: PDB / ID: 6gp1
TitleStructure of mEos4b in the red long-lived dark state
Components(Green to red photoconvertible GFP-like protein EosFP) x 2
KeywordsFLUORESCENT PROTEIN
Function / homology
Function and homology information


bioluminescence / generation of precursor metabolites and energy
Similarity search - Function
Pantoate--beta-alanine Ligase; Chain: A,domain 2 - #40 / Pantoate--beta-alanine Ligase; Chain: A,domain 2 / Green Fluorescent Protein / Green fluorescent protein / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Beta Barrel / 2-Layer Sandwich ...Pantoate--beta-alanine Ligase; Chain: A,domain 2 - #40 / Pantoate--beta-alanine Ligase; Chain: A,domain 2 / Green Fluorescent Protein / Green fluorescent protein / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Green to red photoconvertible GFP-like protein EosFP
Similarity search - Component
Biological speciesLobophyllia hemprichii (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.504 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 CenterUMS 3518 CNRS-CEA-UGA-EMBL France
ANR-10-INBS-05-02 France
ANR-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 / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Polymer sequence / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_2 / entity / entity_poly / entity_poly_seq / pdbx_poly_seq_scheme / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_mod_residue / struct_conn / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _atom_site.auth_atom_id / _atom_site.auth_comp_id ..._atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity_poly.pdbx_seq_one_letter_code / _entity_poly_seq.mon_id / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_assembly.details / _pdbx_struct_assembly_prop.value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_label_comp_id / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end
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 / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id / _struct_conn.ptnr1_label_atom_id
Revision 3.1Jan 17, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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
B: Green to red photoconvertible GFP-like protein EosFP


Theoretical massNumber of molelcules
Total (without water)29,5662
Polymers29,5662
Non-polymers00
Water6,215345
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4780 Å2
ΔGint-24 kcal/mol
Surface area10220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.700, 58.290, 104.030
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 to red photoconvertible GFP-like protein EosFP


Mass: 10479.805 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) / Strain (production host): JM109(DE3) / References: UniProt: Q5S6Z9
#2: Protein Green to red photoconvertible GFP-like protein EosFP


Mass: 19086.492 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) / Strain (production host): JM109(DE3) / References: UniProt: Q5S6Z9
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 345 / 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: 1.99 Å3/Da / Density % sol: 38.05 %
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-F / Detector: PIXEL / Date: Jun 27, 2016
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.3→32.241 Å / Num. obs: 56087 / % possible obs: 97.7 % / Redundancy: 3.599 % / Biso Wilson estimate: 12.4 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.047 / Rrim(I) all: 0.054 / Χ2: 0.981 / Net I/σ(I): 16.52 / Num. measured all: 201864 / Scaling rejects: 3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.3-1.332.7530.4742.1411200420340690.7410.57796.8
1.33-1.373.6040.4452.7614523406840300.8090.51999.1
1.37-1.413.6670.373.4414404397639280.8680.4398.8
1.41-1.453.6180.3044.1213838385938250.9110.35499.1
1.45-1.53.4510.2394.9912710374336830.9390.2898.4
1.5-1.553.6640.1876.5113196363036020.9610.21899.2
1.55-1.613.7240.1527.9613099354335170.9740.17699.3
1.61-1.683.7120.1349.1912339336233240.9810.15598.9
1.68-1.753.5340.10711.1411276324431910.9860.12598.4
1.75-1.843.5740.08214.0310944311030620.9920.09598.5
1.84-1.943.780.06318.8911041297529210.9960.07298.2
1.94-2.063.8150.04824.1410388279127230.9970.05697.6
2.06-2.23.6770.03828.39428263925640.9980.04497.2
2.2-2.373.6280.03530.848732248524070.9980.04196.9
2.37-2.63.8950.03235.688603228622090.9980.03796.6
2.6-2.913.8670.02840.537599208119650.9990.03294.4
2.91-3.363.5290.02445.916115184817330.9990.02793.8
3.36-4.113.8590.01958.025811159215060.9990.02194.6
4.11-5.813.6960.01659.6242731253115610.01992.3
5.81-32.2413.490.0254.0623457436720.9990.02390.4

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.11refinement
PDB_EXTRACT3.24data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6GP0

6gp0


Resolution: 1.504→32.241 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 34.16
RfactorNum. reflection% reflection
Rfree0.3043 1595 4.89 %
Rwork0.2489 --
obs0.2516 32629 85.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 55.31 Å2 / Biso mean: 17.2628 Å2 / Biso min: 6.77 Å2
Refinement stepCycle: final / Resolution: 1.504→32.241 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1784 0 0 345 2129
Biso mean---26.63 -
Num. residues----221
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071935
X-RAY DIFFRACTIONf_angle_d0.9412629
X-RAY DIFFRACTIONf_chiral_restr0.06262
X-RAY DIFFRACTIONf_plane_restr0.006352
X-RAY DIFFRACTIONf_dihedral_angle_d11.8121548
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.504-1.55260.46561110.42312318242971
1.5526-1.60810.48681400.39192748288884
1.6081-1.67250.44991420.36612848299087
1.6725-1.74860.33631630.31712863302688
1.7486-1.84070.36061440.28522932307689
1.8407-1.95610.32791570.25972905306289
1.9561-2.10710.31671430.23922949309290
2.1071-2.31910.3161780.24472923310189
2.3191-2.65450.3111480.24732874302287
2.6545-3.34380.29391410.2252859300085
3.3438-32.24850.19971280.18632815294380

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