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- PDB-2vvh: IrisFP fluorescent protein in its green form, cis conformation -

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Basic information

Entry
Database: PDB / ID: 2vvh
TitleIrisFP fluorescent protein in its green form, cis conformation
ComponentsGreen to red photoconvertible GFP-like protein EosFP
KeywordsFLUORESCENT PROTEIN / PHOTOACTIVATION / PHOTOCONVERSION / OPTICAL HIGHLIGHTERS / MICROSPECTROPHOTOMETRY / EOSFP / PHOTOCHROMISM / PHOTOSWITCHING
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: 1.8 Å
AuthorsAdam, V. / Lelimousin, M. / Boehme, S. / Desfonds, G. / Nienhaus, K. / Field, M.J. / Wiedenmann, J. / McSweeney, S. / Nienhaus, G.U. / Bourgeois, D.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2008
Title: Structural Characterization of Irisfp, an Optical Highlighter Undergoing Multiple Photo-Induced Transformations.
Authors: Adam, V. / Lelimousin, M. / Boehme, S. / Desfonds, G. / Nienhaus, K. / Field, M.J. / Wiedenmann, J. / Mcsweeney, S. / Nienhaus, G.U. / Bourgeois, D.
History
DepositionJun 9, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 11, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 6, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp ..._exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Oct 23, 2019Group: Data collection / Database references / Other / Category: pdbx_database_status / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_sf / _struct_ref_seq_dif.details
Revision 2.0Sep 1, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_2 / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / pdbx_poly_seq_scheme / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_mod_residue / pdbx_validate_polymer_linkage / pdbx_validate_rmsd_bond / struct_conn / struct_ref / struct_ref_seq / 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 / _atom_site.type_symbol / _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.pdbx_description / _entity_poly.pdbx_seq_one_letter_code / _entity_poly_seq.mon_id / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_seq_type / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly_prop.value / _pdbx_struct_mod_residue.auth_comp_id / _pdbx_struct_mod_residue.details / _pdbx_struct_mod_residue.label_comp_id / _pdbx_validate_polymer_linkage.auth_comp_id_2 / _pdbx_validate_rmsd_bond.auth_comp_id_1 / _pdbx_validate_rmsd_bond.auth_comp_id_2
Revision 3.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_polymer_linkage / 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 / _pdbx_validate_polymer_linkage.auth_atom_id_2 / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id
Revision 3.1Dec 13, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 3.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 11-STRANDED BARREL THIS IS REPRESENTED BY A 12-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 11-STRANDED BARREL THIS IS REPRESENTED BY A 12-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 11-STRANDED BARREL THIS IS REPRESENTED BY A 12-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "DA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 11-STRANDED BARREL THIS IS REPRESENTED BY A 12-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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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
C: Green to red photoconvertible GFP-like protein EosFP
D: Green to red photoconvertible GFP-like protein EosFP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,72323
Polymers103,9624
Non-polymers1,76119
Water21,3841187
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12290 Å2
ΔGint-204 kcal/mol
Surface area32840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.340, 96.550, 139.830
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 GFP-like protein EosFP


Mass: 25990.445 Da / Num. of mol.: 4 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lobophyllia hemprichii (invertebrata) / Plasmid: PQE32 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): M15PREP4 / References: UniProt: Q5S6Z9
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-SO3 / SULFITE ION


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


Mass: 18.015 Da / Num. of mol.: 1187 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, PHE 173 TO SER ENGINEERED RESIDUE IN CHAIN A, PHE 191 TO LEU ...ENGINEERED RESIDUE IN CHAIN A, PHE 173 TO SER ENGINEERED RESIDUE IN CHAIN A, PHE 191 TO LEU ENGINEERED RESIDUE IN CHAIN B, PHE 173 TO SER ENGINEERED RESIDUE IN CHAIN B, PHE 191 TO LEU ENGINEERED RESIDUE IN CHAIN C, PHE 173 TO SER ENGINEERED RESIDUE IN CHAIN C, PHE 191 TO LEU ENGINEERED RESIDUE IN CHAIN D, PHE 173 TO SER ENGINEERED RESIDUE IN CHAIN D, PHE 191 TO LEU
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: 2.44 Å3/Da / Density % sol: 49.12 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8.4
Details: CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE, BICINE, PH 8.4, VAPOR DIFFUSION, TEMPERATURE 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 16, 2007
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 1.8→45.6 Å / Num. obs: 108316 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 29.6 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 19.06
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 3.46 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ZUX

1zux


Resolution: 1.8→45.64 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.939 / SU B: 2.596 / SU ML: 0.081 / Cross valid method: THROUGHOUT / ESU R: 0.119 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21889 5416 5 %RANDOM
Rwork0.18486 ---
obs0.18656 102896 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.109 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.8→45.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7136 0 91 1187 8414
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0227565
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2311.97410245
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2165927
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.23524.18366
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.517151279
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.8921536
X-RAY DIFFRACTIONr_chiral_restr0.0740.21036
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025820
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1830.23482
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2970.24938
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.10.21065
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1210.255
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2480.234
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6241.54601
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.74127190
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.1233397
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.7274.53024
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.308 395
Rwork0.275 7507

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