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- PDB-5fvi: Structure of IrisFP in mineral grease at 100 K. -

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Basic information

Entry
Database: PDB / ID: 5fvi
TitleStructure of IrisFP in mineral grease at 100 K.
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
Green to red photoconvertible GFP-like protein EosFP
Similarity search - Component
Biological speciesLobophyllia hemprichii (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.397 Å
AuthorsColletier, J.P. / Gallat, F.X. / Coquelle, N. / Weik, M.
CitationJournal: J.Phys.Chem.Lett. / Year: 2016
Title: Serial Femtosecond Crystallography and Ultrafast Absorption Spectroscopy of the Photoswitchable Fluorescent Protein Irisfp.
Authors: Colletier, J. / Sliwa, M. / Gallat, F. / Sugahara, M. / Guillon, V. / Schiro, G. / Coquelle, N. / Woodhouse, J. / Roux, L. / Gotthard, G. / Royant, A. / Uriarte, L.M. / Ruckebusch, C. / ...Authors: Colletier, J. / Sliwa, M. / Gallat, F. / Sugahara, M. / Guillon, V. / Schiro, G. / Coquelle, N. / Woodhouse, J. / Roux, L. / Gotthard, G. / Royant, A. / Uriarte, L.M. / Ruckebusch, C. / Joti, Y. / Byrdin, M. / Mizohata, E. / Nango, E. / Tanaka, T. / Tono, K. / Yabashi, M. / Adam, V. / Cammarata, M. / Schlichting, I. / Bourgeois, D. / Weik, M.
History
DepositionFeb 7, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 13, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Advisory / Data collection / Category: diffrn_detector / pdbx_unobs_or_zero_occ_atoms / Item: _diffrn_detector.type
Revision 1.2Jan 30, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.3Feb 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Oct 23, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: pdbx_database_status / struct_conn / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _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 / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / database_2 / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / pdbx_poly_seq_scheme / pdbx_struct_assembly_prop / pdbx_struct_mod_residue / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / pdbx_validate_rmsd_angle / struct_conn / struct_ref / struct_ref_seq_dif / struct_sheet / struct_site
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.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.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_prop.value / _pdbx_struct_mod_residue.auth_comp_id / _pdbx_struct_mod_residue.details / _pdbx_struct_mod_residue.label_comp_id / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_comp_id_1 / _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.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq_dif.align_id / _struct_ref_seq_dif.details / _struct_ref_seq_dif.mon_id / _struct_ref_seq_dif.pdbx_pdb_strand_id / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 3.0Nov 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_torsion / 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 / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id
Revision 3.1Jan 10, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 3.2Nov 6, 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 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)104,62927
Polymers102,4204
Non-polymers2,20923
Water16,484915
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12290 Å2
ΔGint-269 kcal/mol
Surface area33250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.580, 95.940, 139.940
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: 25604.979 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.: 23 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 915 / 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: 2.7 Å3/Da / Density % sol: 54.43 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 3 M AMMONIUM SULFATE, 100MM BICINE, PH 8.2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.99
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 42023 / % possible obs: 99.4 % / Observed criterion σ(I): 2.5 / Redundancy: 5.53 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 10.93
Reflection shellResolution: 2.4→2.46 Å / Redundancy: 5.23 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 2.58 / % possible all: 95.7

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VVH

2vvh


Resolution: 2.397→47.97 Å / SU ML: 0.3 / σ(F): 1.36 / Phase error: 24.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2117 2101 5 %
Rwork0.1585 --
obs0.1612 41993 99.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.397→47.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7174 0 115 915 8204
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027942
X-RAY DIFFRACTIONf_angle_d0.57310790
X-RAY DIFFRACTIONf_dihedral_angle_d9.2574683
X-RAY DIFFRACTIONf_chiral_restr0.0441075
X-RAY DIFFRACTIONf_plane_restr0.0031412
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3971-2.45280.36131320.28342504X-RAY DIFFRACTION95
2.4528-2.51420.31871380.24372604X-RAY DIFFRACTION99
2.5142-2.58210.25011370.21232627X-RAY DIFFRACTION100
2.5821-2.65810.3221390.18932640X-RAY DIFFRACTION100
2.6581-2.74390.26681400.18422655X-RAY DIFFRACTION100
2.7439-2.8420.25091380.17652626X-RAY DIFFRACTION100
2.842-2.95570.26131390.17422644X-RAY DIFFRACTION100
2.9557-3.09020.24741410.16822669X-RAY DIFFRACTION100
3.0902-3.25310.18591390.14242650X-RAY DIFFRACTION100
3.2531-3.45690.1861400.13822656X-RAY DIFFRACTION100
3.4569-3.72370.17921400.12672654X-RAY DIFFRACTION99
3.7237-4.09830.16691420.12322694X-RAY DIFFRACTION100
4.0983-4.69090.1661420.11492695X-RAY DIFFRACTION100
4.6909-5.90830.15031440.14192731X-RAY DIFFRACTION100
5.9083-47.97960.25191500.20182843X-RAY DIFFRACTION99

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