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Entry
Database: PDB / ID: 7qlj
TitleTrans structure of rsKiiro Illuminated at 290 K
ComponentsrsKiiro
KeywordsFLUORESCENT PROTEIN / rsKiiro
Function / homologyGreen fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / generation of precursor metabolites and energy / Green to red photoconvertible GFP-like protein EosFP
Function and homology information
Biological speciesLobophyllia hemprichii (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.02 Å
Authorsvan Thor, J.J. / Baxter, J.M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/P00752X/1 United Kingdom
CitationJournal: Nat.Chem. / Year: 2023
Title: Optical control of ultrafast structural dynamics in a fluorescent protein.
Authors: Hutchison, C.D.M. / Baxter, J.M. / Fitzpatrick, A. / Dorlhiac, G. / Fadini, A. / Perrett, S. / Maghlaoui, K. / Lefevre, S.B. / Cordon-Preciado, V. / Ferreira, J.L. / Chukhutsina, V.U. / ...Authors: Hutchison, C.D.M. / Baxter, J.M. / Fitzpatrick, A. / Dorlhiac, G. / Fadini, A. / Perrett, S. / Maghlaoui, K. / Lefevre, S.B. / Cordon-Preciado, V. / Ferreira, J.L. / Chukhutsina, V.U. / Garratt, D. / Barnard, J. / Galinis, G. / Glencross, F. / Morgan, R.M. / Stockton, S. / Taylor, B. / Yuan, L. / Romei, M.G. / Lin, C.Y. / Marangos, J.P. / Schmidt, M. / Chatrchyan, V. / Buckup, T. / Morozov, D. / Park, J. / Park, S. / Eom, I. / Kim, M. / Jang, D. / Choi, H. / Hyun, H. / Park, G. / Nango, E. / Tanaka, R. / Owada, S. / Tono, K. / DePonte, D.P. / Carbajo, S. / Seaberg, M. / Aquila, A. / Boutet, S. / Barty, A. / Iwata, S. / Boxer, S.G. / Groenhof, G. / van Thor, J.J.
History
DepositionDec 20, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 9, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2022Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 30, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Dec 28, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / citation_author / entity / entity_poly / entity_poly_seq / pdbx_entity_instance_feature / pdbx_initial_refinement_model / pdbx_poly_seq_scheme / pdbx_struct_mod_residue / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / pdbx_validate_torsion / 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.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.id / _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 / _chem_comp.type / _citation_author.identifier_ORCID / _entity.formula_weight / _entity.pdbx_description / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_poly_seq.mon_id / _pdbx_entity_instance_feature.auth_comp_id / _pdbx_entity_instance_feature.comp_id / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_comp_id_1 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_end
Revision 3.0Apr 5, 2023Group: Atomic model / Database references / Source and taxonomy
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / entity_src_gen / 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.label_atom_id / _atom_site.occupancy / _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_label_atom_id / _entity_src_gen.gene_src_common_name / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.seq_align_end / _struct_ref_seq_dif.db_mon_id / _struct_ref_seq_dif.details / _struct_ref_seq_dif.pdbx_seq_db_seq_num
Revision 3.1Aug 16, 2023Group: Data collection / Database references
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Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 3.2Aug 23, 2023Group: Database references / Structure summary / Category: citation / citation_author / entity_name_com
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 4.0Nov 15, 2023Group: Atomic model / Data collection / Database references
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / citation
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 ..._chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: rsKiiro
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2492
Polymers25,1521
Non-polymers961
Water4,684260
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.747, 73.524, 78.106
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein rsKiiro / Green to red photoconvertible GFP-like protein EosFP / rsKiiro


Mass: 25152.490 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lobophyllia hemprichii (invertebrata) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5S6Z9
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 260 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.21 Å3/Da / Density % sol: 44.29 %
Crystal growTemperature: 295 K / Method: batch mode / pH: 8.4
Details: 0.2 M lithium sulfate, 0.1 M Tris-Cl, 25 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 1.02→39.053 Å / Num. obs: 112855 / % possible obs: 98.9 % / Redundancy: 6.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.061 / Net I/σ(I): 12.8
Reflection shellResolution: 1.02→1.039 Å / Rmerge(I) obs: 0.777 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 5645 / CC1/2: 0.593

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
autoPROCdata reduction
STARANISOdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5OOZ, 5OQA

5ooz

5oqa


Resolution: 1.02→39.053 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.977 / SU B: 0.579 / SU ML: 0.013 / Cross valid method: FREE R-VALUE / ESU R: 0.02 / ESU R Free: 0.021
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1367 5501 4.875 %
Rwork0.1186 107351 -
all0.119 --
obs-112852 98.892 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 11.113 Å2
Baniso -1Baniso -2Baniso -3
1-0.029 Å2-0 Å2-0 Å2
2---0.16 Å20 Å2
3---0.132 Å2
Refinement stepCycle: LAST / Resolution: 1.02→39.053 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1770 0 5 260 2035
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0132066
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161888
X-RAY DIFFRACTIONr_angle_refined_deg2.5461.7092818
X-RAY DIFFRACTIONr_angle_other_deg1.5421.6114404
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9795270
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.32123.273110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.75215364
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.577159
X-RAY DIFFRACTIONr_chiral_restr0.120.2253
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022637
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02491
X-RAY DIFFRACTIONr_nbd_refined0.2030.2343
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1920.21777
X-RAY DIFFRACTIONr_nbtor_refined0.1810.2937
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0960.21145
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2060.2176
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0170.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.5820.221
X-RAY DIFFRACTIONr_nbd_other0.1880.267
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2350.214
X-RAY DIFFRACTIONr_mcbond_it1.910.828972
X-RAY DIFFRACTIONr_mcbond_other1.9050.82971
X-RAY DIFFRACTIONr_mcangle_it2.2491.2441232
X-RAY DIFFRACTIONr_mcangle_other2.2491.2531233
X-RAY DIFFRACTIONr_scbond_it2.6691.1441094
X-RAY DIFFRACTIONr_scbond_other2.6641.1441091
X-RAY DIFFRACTIONr_scangle_it2.9351.5921569
X-RAY DIFFRACTIONr_scangle_other2.921.5871564
X-RAY DIFFRACTIONr_lrange_it3.52311.0912315
X-RAY DIFFRACTIONr_lrange_other3.2610.4472252
X-RAY DIFFRACTIONr_rigid_bond_restr4.67533952
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.02-1.0460.2444060.247517X-RAY DIFFRACTION94.8181
1.046-1.0750.2023880.1937567X-RAY DIFFRACTION97.8234
1.075-1.1060.1643940.1557371X-RAY DIFFRACTION98.0801
1.106-1.140.1283620.1217229X-RAY DIFFRACTION98.4183
1.14-1.1780.1363110.1127029X-RAY DIFFRACTION98.6692
1.178-1.2190.1273570.1086787X-RAY DIFFRACTION98.9748
1.219-1.2650.1243450.1036577X-RAY DIFFRACTION99.1264
1.265-1.3170.1123500.0936304X-RAY DIFFRACTION99.3579
1.317-1.3750.1133060.0856155X-RAY DIFFRACTION99.3847
1.375-1.4420.1072940.0795838X-RAY DIFFRACTION99.3197
1.442-1.520.1053100.0795562X-RAY DIFFRACTION99.83
1.52-1.6130.1092750.0845335X-RAY DIFFRACTION99.9109
1.613-1.7240.1192390.0894983X-RAY DIFFRACTION99.9617
1.724-1.8620.1062600.0934665X-RAY DIFFRACTION100
1.862-2.0390.1162330.1014307X-RAY DIFFRACTION100
2.039-2.280.1331870.1093938X-RAY DIFFRACTION100
2.28-2.6320.1391730.1273478X-RAY DIFFRACTION100
2.632-3.2230.1481430.1382981X-RAY DIFFRACTION99.9041
3.223-4.5540.153980.1322353X-RAY DIFFRACTION100
4.554-39.0530.225700.1961375X-RAY DIFFRACTION99.9308

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