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- PDB-5fvg: Structure of IrisFP at 100 K. -

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Basic information

Entry
Database: PDB / ID: 5fvg
TitleStructure of IrisFP at 100 K.
ComponentsGreen to red photoconvertible GFP-like protein EosFP
KeywordsFLUORESCENT PROTEIN / FLURESCENT 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: 1.9 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 1.0Jan 11, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
Revision 1.2Jan 30, 2019Group: Data collection / Derived calculations / Experimental preparation
Category: exptl_crystal_grow / struct_conn / 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 / 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_validate_close_contact / 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 / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq_dif.details / _struct_ref_seq_dif.mon_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_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
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 **-STRANDED BARREL THIS IS REPRESENTED BY A **-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN -3-STRANDED BARREL THIS IS REPRESENTED BY A -2-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "CA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN -3-STRANDED BARREL THIS IS REPRESENTED BY A -2-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "DA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN -3-STRANDED BARREL THIS IS REPRESENTED BY A -2-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)104,24523
Polymers102,4204
Non-polymers1,82519
Water14,070781
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11780 Å2
ΔGint-231 kcal/mol
Surface area33330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.090, 96.320, 140.190
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.: 19 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 781 / 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: 2.7 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 PILATUS3 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: 1.9→50 Å / Num. obs: 86705 / % possible obs: 99 % / Observed criterion σ(I): 1.5 / Redundancy: 4.4 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 9.2
Reflection shellResolution: 1.9→1.96 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 1.67 / % possible all: 99.7

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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: 1.9→45.869 Å / SU ML: 0.24 / σ(F): 1.35 / Phase error: 29.27 / Stereochemistry target values: ML
Details: A LARGE STRETCH OF POSITIVE ELECTRON DENS WAS OBSERVED AT THE INTERFACE BETWEEN THE FOUR MONOMERS IN A TETRAM NOT BE ASSIGNED TO A KNOWN COMPONENT OF THE MOTHER LIQUOR SOLUTION, AND ...Details: A LARGE STRETCH OF POSITIVE ELECTRON DENS WAS OBSERVED AT THE INTERFACE BETWEEN THE FOUR MONOMERS IN A TETRAM NOT BE ASSIGNED TO A KNOWN COMPONENT OF THE MOTHER LIQUOR SOLUTION, AND THEREFORE WAS NOT MODELLED. THIS DENSITY COULD CORRESPOND TO A
RfactorNum. reflection% reflection
Rfree0.2345 4113 5 %
Rwork0.19 --
obs0.1923 82249 97.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→45.869 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7164 0 95 781 8040
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077878
X-RAY DIFFRACTIONf_angle_d0.90110695
X-RAY DIFFRACTIONf_dihedral_angle_d18.1584634
X-RAY DIFFRACTIONf_chiral_restr0.0581067
X-RAY DIFFRACTIONf_plane_restr0.0051396
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.92240.40181390.35432639X-RAY DIFFRACTION97
1.9224-1.94580.37781400.34392662X-RAY DIFFRACTION98
1.9458-1.97040.37371390.32022646X-RAY DIFFRACTION97
1.9704-1.99640.38551350.30252558X-RAY DIFFRACTION94
1.9964-2.02370.321380.28212628X-RAY DIFFRACTION97
2.0237-2.05260.37681410.27372673X-RAY DIFFRACTION97
2.0526-2.08330.28281390.25832645X-RAY DIFFRACTION98
2.0833-2.11580.32961420.24942685X-RAY DIFFRACTION99
2.1158-2.15050.29861400.23262673X-RAY DIFFRACTION98
2.1505-2.18760.30161390.22762634X-RAY DIFFRACTION97
2.1876-2.22740.30471400.22532663X-RAY DIFFRACTION97
2.2274-2.27020.27471400.20892648X-RAY DIFFRACTION98
2.2702-2.31650.24151410.21312695X-RAY DIFFRACTION98
2.3165-2.36690.31661430.20652700X-RAY DIFFRACTION98
2.3669-2.4220.25381400.21042668X-RAY DIFFRACTION98
2.422-2.48250.24791420.21092695X-RAY DIFFRACTION98
2.4825-2.54970.26991380.2062624X-RAY DIFFRACTION96
2.5497-2.62470.26251420.20142686X-RAY DIFFRACTION98
2.6247-2.70940.24931430.18262714X-RAY DIFFRACTION99
2.7094-2.80620.23341410.18552700X-RAY DIFFRACTION99
2.8062-2.91850.25631440.18692732X-RAY DIFFRACTION99
2.9185-3.05130.28391420.19882715X-RAY DIFFRACTION99
3.0513-3.21220.23061450.17532743X-RAY DIFFRACTION99
3.2122-3.41340.22721440.17162743X-RAY DIFFRACTION99
3.4134-3.67680.20191440.15272738X-RAY DIFFRACTION99
3.6768-4.04660.16511440.13662724X-RAY DIFFRACTION98
4.0466-4.63170.15251470.12072791X-RAY DIFFRACTION99
4.6317-5.83360.14621480.14182812X-RAY DIFFRACTION99
5.8336-45.88190.22291530.20382902X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 8.7963 Å / Origin y: 2.4575 Å / Origin z: -50.9821 Å
111213212223313233
T0.4365 Å20.0012 Å2-0.0096 Å2-0.1441 Å20.013 Å2--0.1559 Å2
L0.3323 °2-0.0197 °2-0.0765 °2-0.5947 °20.2077 °2--0.5297 °2
S0.0349 Å °0.0212 Å °0.0468 Å °-0.1074 Å °-0.0035 Å °0.026 Å °-0.1006 Å °0.0524 Å °-0.0336 Å °
Refinement TLS groupSelection details: ALL

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