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- PDB-6yls: mEos4b - Directionality of Optical Properties of Fluorescent Proteins -

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Basic information

Entry
Database: PDB / ID: 6yls
TitlemEos4b - Directionality of Optical Properties of Fluorescent Proteins
ComponentsGreen to red photoconvertible GFP-like protein EosFP
KeywordsFLUORESCENT PROTEIN / mEos4b
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 / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsMyskova, J. / Rybakova, O. / Brynda, J. / Lazar, J.
Funding support Czech Republic, 1items
OrganizationGrant numberCountry
Ministry of Education, Youth and Sports of the Czech RepublicCZ.02.1.01/0.0/0.0/16_019/0000729 Czech Republic
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Directionality of light absorption and emission in representative fluorescent proteins.
Authors: Myskova, J. / Rybakova, O. / Brynda, J. / Khoroshyy, P. / Bondar, A. / Lazar, J.
History
DepositionApr 7, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 16, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Sep 1, 2021Group: Database references / Derived calculations ...Database references / Derived calculations / Source and taxonomy / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / entity / entity_src_gen / pdbx_struct_mod_residue / struct_conn / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _chem_comp.name / _chem_comp.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _entity_src_gen.gene_src_common_name / _struct_conn.pdbx_leaving_atom_flag / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_db_accession / _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_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_end
Revision 2.0Nov 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
Revision 2.1Jan 24, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 2.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)26,9483
Polymers26,8891
Non-polymers582
Water3,567198
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-17 kcal/mol
Surface area10330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.510, 70.510, 90.600
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: 26889.395 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lobophyllia hemprichii (invertebrata) / Production host: Escherichia coli (E. coli) / References: UniProt: Q5S6Z9
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.12 Å3/Da / Density % sol: 42.01 %
Description: A - long axis of crystal B, C - diagonal to the faces of the crystal
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: PEG 6000, tri-sodium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54187 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Nov 30, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 1.55→35.44 Å / Num. obs: 61581 / % possible obs: 89 % / Redundancy: 2.456 % / Biso Wilson estimate: 20.974 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.065 / Rrim(I) all: 0.076 / Χ2: 1.106 / Net I/σ(I): 9.15 / Num. measured all: 151232 / Scaling rejects: 461
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
1.55-1.591.2260.3240.982142515217470.7490.45533.9
1.59-1.631.1970.3121.124664496438950.7740.4478.5
1.63-1.681.2330.2421.375229487442400.8460.34187
1.68-1.731.2550.2221.675234469641710.8670.31488.8
1.73-1.791.2960.18225355455741320.9040.25790.7
1.79-1.851.3410.1562.585512445241100.930.2292.3
1.85-1.921.3660.1684.275250427938430.9060.23589.8
1.92-21.5940.164.326089405938200.9540.21194.1
2-2.091.8730.1365.867038395437570.9680.17195
2.09-2.192.3290.1586.998451373036280.9480.19697.3
2.19-2.312.7310.1737.589618357035220.950.21498.7
2.31-2.453.1420.1359.0110487339633380.9740.16298.3
2.45-2.623.1830.1110.939939317031230.9830.13298.5
2.62-2.833.7480.08914.4811049297429480.9910.10499.1
2.83-3.14.320.06819.1711678271827030.9960.07899.4
3.1-3.474.5320.05225.2711177247624660.9970.05999.6
3.47-44.9660.04630.5110602214721350.9980.05299.4
4-4.95.3040.03933.959691183618270.9990.04399.5
4.9-6.935.4520.04231.577687141214100.9980.04799.9
6.93-35.445.6660.04133.7543407777660.9990.04598.6

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
REFMAC5.8.0103refinement
PDB_EXTRACT3.25data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3s05

3s05


Resolution: 1.55→35.44 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.921 / SU B: 2.275 / SU ML: 0.083 / SU R Cruickshank DPI: 0.0839 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.084 / ESU R Free: 0.084
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.214 1027 3 %RANDOM
Rwork0.1857 ---
obs0.1866 33203 93.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 193.88 Å2 / Biso mean: 21.084 Å2 / Biso min: 9.69 Å2
Baniso -1Baniso -2Baniso -3
1--0.65 Å20 Å2-0 Å2
2--0.58 Å20 Å2
3---0.08 Å2
Refinement stepCycle: final / Resolution: 1.55→35.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1755 0 2 198 1955
Biso mean--23.17 26 -
Num. residues----220
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0191861
X-RAY DIFFRACTIONr_bond_other_d0.0030.021687
X-RAY DIFFRACTIONr_angle_refined_deg1.7651.9552530
X-RAY DIFFRACTIONr_angle_other_deg1.08833909
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8545237
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.12124.72591
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.91315308
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.394157
X-RAY DIFFRACTIONr_chiral_restr0.1060.2259
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022147
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02441
LS refinement shellResolution: 1.55→1.59 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 43 -
Rwork0.249 1404 -
all-1447 -
obs--54.24 %

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