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- PDB-4ljb: Structure of a photobleached state of IrisFP under high intensity... -

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Basic information

Entry
Database: PDB / ID: 4ljb
TitleStructure of a photobleached state of IrisFP under high intensity laser-light
ComponentsGreen to red photoconvertible GPF-like protein EosFP
KeywordsFLUORESCENT PROTEIN / Photobleaching / Beta-Barrel / Decarboxylation
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
SULFITE ION / Green to red photoconvertible GFP-like protein EosFP
Similarity search - Component
Biological speciesLobophyllia hemprichii (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9019 Å
AuthorsDuan, C. / Adam, V. / Byrdin, M. / Ridard, J. / Kieffer-Jacquinod, S. / Morlot, C. / Arcizet, D. / Demachy, I. / Bourgeois, D.
CitationJournal: J.Am.Chem.Soc. / Year: 2013
Title: Structural evidence for a two-regime photobleaching mechanism in a reversibly switchable fluorescent protein.
Authors: Duan, C. / Adam, V. / Byrdin, M. / Ridard, J. / Kieffer-Jaquinod, S. / Morlot, C. / Arcizet, D. / Demachy, I. / Bourgeois, D.
History
DepositionJul 4, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2013Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / pdbx_validate_rmsd_angle / 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 / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id
Revision 2.1Oct 30, 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 GPF-like protein EosFP
B: Green to red photoconvertible GPF-like protein EosFP
C: Green to red photoconvertible GPF-like protein EosFP
D: Green to red photoconvertible GPF-like protein EosFP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,11520
Polymers104,6264
Non-polymers1,48916
Water5,639313
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8440 Å2
ΔGint-24 kcal/mol
Surface area33090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.099, 96.416, 140.033
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 GPF-like protein EosFP


Mass: 26156.557 Da / Num. of mol.: 4
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-SO3 / SULFITE ION


Mass: 80.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 313 / 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: 2.77 Å3/Da / Density % sol: 55.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 2.1M ammonium sulfate, 0.1M bicine, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 15, 2012
RadiationMonochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.9→47.32 Å / Num. all: 90548 / Num. obs: 91193 / % possible obs: 99.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.2 % / Biso Wilson estimate: 34.9 Å2 / Rsym value: 0.068
Reflection shellResolution: 1.9→2 Å / % possible all: 99.2

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Processing

Software
NameVersionClassification
MxCuBEdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VVH - IRISFP FLUORESCENT PROTEIN IN ITS GREEN FORM, CIS CONFORMATION

2vvh


Resolution: 1.9019→10.013 Å / SU ML: 0.28 / σ(F): 0 / Phase error: 45.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3839 3938 5.02 %
Rwork0.3393 --
obs0.3416 78454 85.86 %
all-89037 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9019→10.013 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7121 0 77 313 7511
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097390
X-RAY DIFFRACTIONf_angle_d1.5239962
X-RAY DIFFRACTIONf_dihedral_angle_d16.8082693
X-RAY DIFFRACTIONf_chiral_restr0.0991010
X-RAY DIFFRACTIONf_plane_restr0.0071281
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9019-1.9250.58641360.47862355X-RAY DIFFRACTION77
1.925-1.94920.53051440.42322906X-RAY DIFFRACTION95
1.9492-1.97460.50261420.39782885X-RAY DIFFRACTION94
1.9746-2.00150.45441460.38432904X-RAY DIFFRACTION93
2.0015-2.02980.43481490.36922826X-RAY DIFFRACTION93
2.0298-2.05990.46861500.36212831X-RAY DIFFRACTION92
2.0599-2.09180.47361340.38742633X-RAY DIFFRACTION85
2.0918-2.12570.45711530.36352758X-RAY DIFFRACTION91
2.1257-2.1620.44581430.35892789X-RAY DIFFRACTION90
2.162-2.2010.45041480.35382722X-RAY DIFFRACTION89
2.201-2.24280.4471430.36932801X-RAY DIFFRACTION90
2.2428-2.28810.42311350.38092383X-RAY DIFFRACTION79
2.2881-2.33720.47341370.37262682X-RAY DIFFRACTION87
2.3372-2.39090.48021320.37592624X-RAY DIFFRACTION85
2.3909-2.44980.4581390.38292574X-RAY DIFFRACTION84
2.4498-2.5150.43211400.39292561X-RAY DIFFRACTION83
2.515-2.58780.44981320.38472536X-RAY DIFFRACTION82
2.5878-2.66980.38451280.37452490X-RAY DIFFRACTION80
2.6698-2.76330.37351420.36512495X-RAY DIFFRACTION81
2.7633-2.87140.441320.36312478X-RAY DIFFRACTION80
2.8714-2.99870.46461220.38332512X-RAY DIFFRACTION81
2.9987-3.15220.3541330.37942527X-RAY DIFFRACTION81
3.1522-3.34270.37251410.33812532X-RAY DIFFRACTION81
3.3427-3.58980.31351380.3252597X-RAY DIFFRACTION83
3.5898-3.9310.37151410.29922552X-RAY DIFFRACTION82
3.931-4.45540.28091450.27372763X-RAY DIFFRACTION87
4.4554-5.45770.25191510.24462826X-RAY DIFFRACTION89
5.4577-10.01350.31291620.27662974X-RAY DIFFRACTION91
Refinement TLS params.Method: refined / Origin x: -9.7783 Å / Origin y: 2.466 Å / Origin z: -19.6889 Å
111213212223313233
T0.2391 Å2-0.001 Å20.0352 Å2-0.0969 Å2-0.0053 Å2--0.0973 Å2
L0.1835 °20.1956 °2-0.1159 °2-0.4023 °2-0.056 °2--0.7117 °2
S0.0282 Å °-0.0159 Å °0.0114 Å °0.103 Å °-0.0435 Å °0.0108 Å °0.0606 Å °-0.0966 Å °0 Å °
Refinement TLS groupSelection details: all

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