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- PDB-4ljc: Structure of an X-ray-induced photobleached state of IrisFP -

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Basic information

Entry
Database: PDB / ID: 4ljc
TitleStructure of an X-ray-induced photobleached state of IrisFP
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: 1.86 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 / chem_comp_atom ...atom_site / 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 / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)105,95518
Polymers104,6264
Non-polymers1,32914
Water12,394688
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8430 Å2
ΔGint-15 kcal/mol
Surface area32430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.102, 96.636, 139.711
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 / Sulfate


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


Mass: 80.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 688 / 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: 2.78 Å3/Da / Density % sol: 55.72 %
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: ID29 / Wavelength: 0.972 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 29, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 1.86→48.41 Å / Num. all: 285214 / Num. obs: 99096 / % possible obs: 99.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Biso Wilson estimate: 24.8 Å2 / Rsym value: 0.062 / Net I/σ(I): 10.4
Reflection shellResolution: 1.86→1.96 Å / % possible all: 98.6

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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: 1.86→19.869 Å / SU ML: 0.24 / σ(F): 0 / Phase error: 26.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.246 4790 4.99 %
Rwork0.2015 --
obs0.2037 95930 97.62 %
all-96895 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.86→19.869 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7100 0 69 688 7857
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0127403
X-RAY DIFFRACTIONf_angle_d1.6319988
X-RAY DIFFRACTIONf_dihedral_angle_d15.8422694
X-RAY DIFFRACTIONf_chiral_restr0.1051017
X-RAY DIFFRACTIONf_plane_restr0.0071280
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.86-1.88110.33041750.32293008X-RAY DIFFRACTION99
1.8811-1.90330.32481500.30793047X-RAY DIFFRACTION98
1.9033-1.92640.38271390.30272964X-RAY DIFFRACTION96
1.9264-1.95080.34831450.29012973X-RAY DIFFRACTION96
1.9508-1.97650.31351720.26233023X-RAY DIFFRACTION98
1.9765-2.00350.30831400.24383061X-RAY DIFFRACTION98
2.0035-2.03210.30181680.24292987X-RAY DIFFRACTION98
2.0321-2.06240.28831560.23723028X-RAY DIFFRACTION98
2.0624-2.09460.27471660.23823074X-RAY DIFFRACTION99
2.0946-2.12890.27451510.23793001X-RAY DIFFRACTION98
2.1289-2.16560.31271780.22933020X-RAY DIFFRACTION98
2.1656-2.20490.26831640.22893042X-RAY DIFFRACTION98
2.2049-2.24720.31131500.23283033X-RAY DIFFRACTION98
2.2472-2.29310.25241520.22753052X-RAY DIFFRACTION99
2.2931-2.34280.28171520.21973055X-RAY DIFFRACTION98
2.3428-2.39720.26391770.22513040X-RAY DIFFRACTION98
2.3972-2.45710.30751660.2282961X-RAY DIFFRACTION97
2.4571-2.52340.29391620.22282984X-RAY DIFFRACTION96
2.5234-2.59750.28371580.22513054X-RAY DIFFRACTION98
2.5975-2.68110.29941750.213015X-RAY DIFFRACTION97
2.6811-2.77670.24441590.20943016X-RAY DIFFRACTION97
2.7767-2.88760.26471480.21783011X-RAY DIFFRACTION96
2.8876-3.01860.26191550.22913013X-RAY DIFFRACTION96
3.0186-3.17710.25771490.2063029X-RAY DIFFRACTION97
3.1771-3.37530.25141680.19072972X-RAY DIFFRACTION96
3.3753-3.63440.20431670.17343008X-RAY DIFFRACTION96
3.6344-3.99750.20031600.15543081X-RAY DIFFRACTION97
3.9975-4.56980.1681430.14383144X-RAY DIFFRACTION98
4.5698-5.73440.17511670.15693159X-RAY DIFFRACTION98
5.7344-19.87030.20481780.17863285X-RAY DIFFRACTION99

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