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Entry
Database: PDB / ID: 5fvf
TitleRoom temperature structure of IrisFP determined by serial femtosecond crystallography.
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
AMMONIUM ION / Green to red photoconvertible GFP-like protein EosFP
Similarity search - Component
Biological speciesLobophyllia hemprichii (invertebrata)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.75 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 6, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 6, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 26, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.2Nov 14, 2018Group: Data collection / Category: diffrn / diffrn_source
Item: _diffrn.pdbx_serial_crystal_experiment / _diffrn_source.pdbx_wavelength_list
Revision 1.3Jan 30, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.4Feb 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5Oct 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.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.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 / 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

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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)104,28125
Polymers102,4204
Non-polymers1,86121
Water6,197344
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11250 Å2
ΔGint-215 kcal/mol
Surface area35440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.330, 97.760, 142.650
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 / Sulfate


Mass: 96.063 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NH4 / AMMONIUM ION / Ammonium


Mass: 18.038 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H4N
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 344 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54.43 %
Description: DATA WERE COLLECTED BY SERIAL FEMTOSECOND CRYSTALLOGRAPHY. HENCE THE RMERGE REPORTED ABOVE IS IN FACT THE RSPLIT. 10899 PATTERNS WERE INDEXED.
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: 297 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SACLA / Beamline: BL3 / Wavelength: 1.77 / Wavelength: 1.77 Å
DetectorType: MPCCD / Detector: CCD / Date: Feb 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.77 Å / Relative weight: 1
ReflectionResolution: 2.75→50 Å / Num. obs: 30981 / % possible obs: 100 % / Observed criterion σ(I): 0.95 / Redundancy: 159 % / Rmerge(I) obs: 0.22 / Net I/σ(I): 3.39
Reflection shellResolution: 2.75→2.8 Å / Redundancy: 70 % / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 0.95 / % possible all: 100

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Processing

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

2vvh


Resolution: 2.75→46.241 Å / SU ML: 0.44 / σ(F): 1.34 / Phase error: 26.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2391 3062 9.9 %
Rwork0.1759 --
obs0.182 30968 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.75→46.241 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7161 0 97 344 7602
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0147784
X-RAY DIFFRACTIONf_angle_d0.66110528
X-RAY DIFFRACTIONf_dihedral_angle_d13.5922893
X-RAY DIFFRACTIONf_chiral_restr0.0461047
X-RAY DIFFRACTIONf_plane_restr0.0041372
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.7930.45141390.41061267X-RAY DIFFRACTION100
2.793-2.83880.39191450.35891214X-RAY DIFFRACTION100
2.8388-2.88770.3461450.31581245X-RAY DIFFRACTION100
2.8877-2.94020.37931340.28681237X-RAY DIFFRACTION100
2.9402-2.99680.391540.29411254X-RAY DIFFRACTION100
2.9968-3.05790.32861430.26481238X-RAY DIFFRACTION100
3.0579-3.12440.29811220.22541264X-RAY DIFFRACTION100
3.1244-3.19710.27841520.22281241X-RAY DIFFRACTION100
3.1971-3.2770.26471400.21341243X-RAY DIFFRACTION100
3.277-3.36560.29131540.21131258X-RAY DIFFRACTION100
3.3656-3.46460.24181390.20291254X-RAY DIFFRACTION100
3.4646-3.57640.26261230.16651260X-RAY DIFFRACTION100
3.5764-3.70410.22631270.15921271X-RAY DIFFRACTION100
3.7041-3.85240.20011270.15311278X-RAY DIFFRACTION100
3.8524-4.02760.24741430.14761274X-RAY DIFFRACTION100
4.0276-4.23980.211380.15261268X-RAY DIFFRACTION100
4.2398-4.50520.1991340.12681270X-RAY DIFFRACTION100
4.5052-4.85270.19071330.12481288X-RAY DIFFRACTION100
4.8527-5.34040.17421430.12231298X-RAY DIFFRACTION100
5.3404-6.11170.22021460.15521289X-RAY DIFFRACTION100
6.1117-7.69440.21171410.18431308X-RAY DIFFRACTION100
7.6944-46.24720.25991400.19431387X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.65470.21-0.90980.8795-0.77182.36260.0278-0.110.02690.2163-0.04860.21570.0729-0.211700.47910.0511-0.04410.5709-0.02670.6528-10.49579.5933-28.1338
21.4948-0.1326-0.44033.20650.93122.33160.0148-0.00180.1059-0.1697-0.0850.1807-0.23750.042300.5834-0.0234-0.01650.55410.00110.5847-1.049710.1088-36.7649
30.6923-0.56120.50951.13080.5492.24670.3036-0.5336-0.13270.6924-0.3852-0.347-0.12450.105600.85250.0570.02480.5932-0.03250.66461.97888.4404-26.1951
41.33310.6518-0.68110.53310.01751.454-0.09210.0835-0.12990.35080.08360.62940.54220.0506-00.69650.0969-0.16510.80680.00020.8293-19.028-7.9073-59.486
51.75750.14710.37712.8755-0.44231.64750.10180.0619-0.0715-0.138-0.10490.3306-0.021-0.096-00.64140.0478-0.05660.5961-0.04880.6357-8.2222-5.9159-60.1591
61.50171.46190.07451.7075-0.4881.54260.41960.32740.2839-0.7983-0.0008-0.1533-0.3598-0.1154-00.75390.1108-0.09120.7236-0.06510.585-9.1733-5.0976-69.9845
71.95170.3643-1.26831.06070.36961.1925-0.01780.43120.2717-0.4807-0.205-0.609-0.31550.6667-0.00010.8232-0.07080.09070.6861-0.00690.649230.6682-8.0224-71.9821
82.016-1.1139-0.39573.0607-0.76322.51920.24150.32140.1568-0.3881-0.1746-0.38-0.22010.2512-00.5204-0.01330.0450.6446-0.01170.611123.8444-5.1157-70.568
91.01940.75560.10780.72280.48411.01470.0411-0.09010.0438-0.1084-0.02340.00770.02740.015900.69170.0148-0.00360.63890.00940.607415.0792-8.1228-59.978
101.8179-0.52810.82830.2877-0.46270.73340.12390.08830.145-0.53590.06960.1037-0.12820.297400.84030.05190.0190.6881-0.01060.606715.7461-3.2822-70.343
110.99050.2951-0.95542.22741.38452.4090.32110.1671-1.1577-0.4028-0.05370.40620.0429-0.26-00.65040.0140.01640.66190.03320.572617.8422-14.9881-70.8428
120.6629-0.12640.18511.42-0.62351.2560.3118-0.20540.0833-0.3281-0.1609-0.59690.13240.7259-0.03230.5272-0.16240.13950.8685-0.1411.034337.014113.6647-46.7209
130.4712-0.6391-0.21841.17540.4020.1374-0.2934-0.06180.4923-0.06780.7702-0.78870.13991.66430.02660.6192-0.2250.06830.9068-0.0330.89235.928618.5857-43.1821
141.6076-0.2167-0.54411.7210.82350.5725-0.078-0.28370.02460.2015-0.0442-0.7709-0.60950.6937-0.00070.5349-0.1443-0.0360.773-0.08330.701529.739710.6541-39.4164
150.83770.3225-1.09711.35310.31151.8745-0.0476-0.06530.1458-0.30180.0596-0.32090.06240.820300.51880.00910.06240.7377-0.05530.755530.85366.4685-47.5864
160.1504-0.0855-0.04970.11650.05640.0280.80440.63930.4648-0.1704-0.7598-0.1593-1.1579-0.4469-0.00051.27370.13990.04540.68990.02960.689118.415618.004-62.0017
170.6348-0.22280.21480.096-0.16790.5396-0.1877-0.5110.0391-0.10460.70030.0769-0.0477-0.3182-00.7071-0.03820.02510.67660.02160.724518.37159.9689-42.0751
181.50770.5615-0.15880.50230.44210.873-0.465-0.3293-0.00630.57340.4488-0.1934-0.55440.03300.76-0.2384-0.01540.7847-0.01010.542118.714810.204-46.6517
190.7343-0.1566-0.45940.45680.58190.8432-0.0846-0.54070.1851-0.1590.0614-0.4308-0.16960.9043-00.64720.0281-0.05650.8658-0.00290.683727.03258.0635-35.6414
201.3296-0.65460.87050.545-0.37560.58450.1277-0.0620.55110.33610.22680.0865-0.87070.280600.9344-0.19080.08910.7515-0.04140.71826.313320.6963-41.218
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 1 THROUGH 46 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 47 THROUGH 201 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 202 THROUGH 223 )
4X-RAY DIFFRACTION4CHAIN 'B' AND (RESID -1 THROUGH 32 )
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESID 33 THROUGH 201 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 202 THROUGH 223 )
7X-RAY DIFFRACTION7CHAIN 'C' AND (RESID 1 THROUGH 32 )
8X-RAY DIFFRACTION8CHAIN 'C' AND (RESID 33 THROUGH 123 )
9X-RAY DIFFRACTION9CHAIN 'C' AND (RESID 124 THROUGH 166 )
10X-RAY DIFFRACTION10CHAIN 'C' AND (RESID 167 THROUGH 201 )
11X-RAY DIFFRACTION11CHAIN 'C' AND (RESID 202 THROUGH 223 )
12X-RAY DIFFRACTION12CHAIN 'D' AND (RESID 2 THROUGH 32 )
13X-RAY DIFFRACTION13CHAIN 'D' AND (RESID 33 THROUGH 46 )
14X-RAY DIFFRACTION14CHAIN 'D' AND (RESID 47 THROUGH 86 )
15X-RAY DIFFRACTION15CHAIN 'D' AND (RESID 87 THROUGH 123 )
16X-RAY DIFFRACTION16CHAIN 'D' AND (RESID 124 THROUGH 135 )
17X-RAY DIFFRACTION17CHAIN 'D' AND (RESID 136 THROUGH 163 )
18X-RAY DIFFRACTION18CHAIN 'D' AND (RESID 164 THROUGH 179 )
19X-RAY DIFFRACTION19CHAIN 'D' AND (RESID 180 THROUGH 201 )
20X-RAY DIFFRACTION20CHAIN 'D' AND (RESID 202 THROUGH 223 )

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