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- PDB-6goz: Structure of mEos4b in the green long-lived dark state -

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Basic information

Entry
Database: PDB / ID: 6goz
TitleStructure of mEos4b in the green long-lived dark 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: 2.406 Å
AuthorsDe Zitter, E. / Adam, V. / Byrdin, M. / Van Meervelt, L. / Dedecker, P. / Bourgeois, D.
Funding support Belgium, France, 2items
OrganizationGrant numberCountry
Research Foundation - Flanders Belgium
Grenoble Instruct-ERIC CenterUMS 3518 CNRS-CEA-UGA-EMBL France
CitationJournal: J.Am.Chem.Soc. / Year: 2020
Title: Mechanistic Investigations of Green mEos4b Reveal a Dynamic Long-Lived Dark State.
Authors: De Zitter, E. / Ridard, J. / Thedie, D. / Adam, V. / Levy, B. / Byrdin, M. / Gotthard, G. / Van Meervelt, L. / Dedecker, P. / Demachy, I. / Bourgeois, D.
History
DepositionJun 4, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 13, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.0Sep 1, 2021Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / 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_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 / _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 / _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
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 ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9335
Polymers29,5661
Non-polymers3664
Water1,69394
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area940 Å2
ΔGint7 kcal/mol
Surface area10210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.620, 57.660, 102.400
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 62.068 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C2H6O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 94 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.93 Å3/Da / Density % sol: 36.21 %
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 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97903 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: 0.97903 Å / Relative weight: 1
ReflectionResolution: 2.406→38.285 Å / Num. obs: 8804 / % possible obs: 94.1 % / Redundancy: 3.451 % / Biso Wilson estimate: 32.499 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.131 / Rrim(I) all: 0.151 / Χ2: 0.949 / Net I/σ(I): 9.53
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
2.41-2.473.5210.5512.5822326656340.8810.63995.3
2.47-2.543.3940.4723.1221796666420.9050.55196.4
2.54-2.613.4310.4553.2820766366050.9220.53195.1
2.61-2.693.2650.3833.6319076135840.940.44995.3
2.69-2.783.1510.324.2218566175890.9520.37995.5
2.78-2.883.6380.2835.8220415915610.9660.32594.9
2.88-2.983.4530.2695.8818235605280.9770.31294.3
2.98-3.113.5710.236.8318465465170.9720.26594.7
3.11-3.243.5390.1968.4918125355120.9830.22595.7
3.24-3.43.5630.15710.1817035024780.990.1895.2
3.4-3.593.1410.11911.6314674914670.9890.1495.1
3.59-3.83.6260.10715.2615634594310.990.12393.9
3.8-4.073.6860.08916.4814674253980.9960.10293.6
4.07-4.393.5990.07418.9213934133870.9950.08593.7
4.39-4.813.4830.06720.0612123793480.9970.07791.8
4.81-5.383.130.06617.849893463160.9970.07791.3
5.38-6.213.6480.07816.979962992730.9960.08991.3
6.21-7.613.6160.07717.098572672370.9940.08888.8
7.61-10.763.1470.04523.125982171900.9980.05387.6
10.76-38.2853.3930.03528.123631311070.9970.04181.7

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Processing

Software
NameVersionClassification
PHENIX1.15refinement
XDSVersion June 1, 2017data reduction
XSCALEVersion June 1, 2017data scaling
PDB_EXTRACT3.24data extraction
PHENIX1.15phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.406→38.285 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 28.33
RfactorNum. reflection% reflection
Rfree0.2642 881 10.01 %
Rwork0.2015 --
obs0.208 8797 94.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 78.93 Å2 / Biso mean: 33.1639 Å2 / Biso min: 14 Å2
Refinement stepCycle: final / Resolution: 2.406→38.285 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1784 0 24 94 1902
Biso mean--48.28 34.99 -
Num. residues----222
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4061-2.55680.36011450.2801130496
2.5568-2.75410.32951470.2714132095
2.7541-3.03120.27191440.2317129594
3.0312-3.46960.26171480.2028132795
3.4696-4.37030.25121470.1617132894
4.3703-38.2850.2211500.1793134290

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