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- PDB-7qlk: Cis structure intermediate of rsKiiro Illuminated at 200 K -

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Basic information

Entry
Database: PDB / ID: 7qlk
TitleCis structure intermediate of rsKiiro Illuminated at 200 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: 1.458 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 1.0Jul 5, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.title / _citation.year
Revision 1.2Aug 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 2.0Nov 15, 2023Group: Atomic model / Data collection / Database references
Category: atom_site / chem_comp_atom ...atom_site / 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)25,3413
Polymers25,1521
Non-polymers1882
Water3,549197
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.648, 73.746, 78.142
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 197 / 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: 2.25 Å3/Da / Density % sol: 45.33 %
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: I03 / Wavelength: 0.7293 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7293 Å / Relative weight: 1
ReflectionResolution: 1.458→53.691 Å / Num. obs: 34516 / % possible obs: 87 % / Redundancy: 13.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.135 / Net I/σ(I): 10.7
Reflection shellResolution: 1.459→1.546 Å / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1725 / CC1/2: 0.643

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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: 1.458→53.691 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.959 / WRfactor Rfree: 0.2 / WRfactor Rwork: 0.176 / SU B: 1.514 / SU ML: 0.054 / Average fsc free: 0.9274 / Average fsc work: 0.9356 / Cross valid method: FREE R-VALUE / ESU R: 0.078 / ESU R Free: 0.077
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1973 1672 4.844 %
Rwork0.1717 32844 -
all0.173 --
obs-34516 86.735 %
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: 18.663 Å2
Baniso -1Baniso -2Baniso -3
1-0.009 Å20 Å20 Å2
2--0.012 Å2-0 Å2
3----0.021 Å2
Refinement stepCycle: LAST / Resolution: 1.458→53.691 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1747 0 11 197 1955
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0131955
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161804
X-RAY DIFFRACTIONr_angle_refined_deg1.8341.6832657
X-RAY DIFFRACTIONr_angle_other_deg1.4671.6054200
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4585252
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.09222.925106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.25215348
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.7731510
X-RAY DIFFRACTIONr_chiral_restr0.0880.2239
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022267
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02462
X-RAY DIFFRACTIONr_nbd_refined0.2620.2319
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2020.21651
X-RAY DIFFRACTIONr_nbtor_refined0.1740.2838
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0850.2943
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2030.2169
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1280.215
X-RAY DIFFRACTIONr_nbd_other0.1840.248
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3740.225
X-RAY DIFFRACTIONr_mcbond_it1.6931.671930
X-RAY DIFFRACTIONr_mcbond_other1.6891.667929
X-RAY DIFFRACTIONr_mcangle_it2.4182.4941181
X-RAY DIFFRACTIONr_mcangle_other2.422.4991182
X-RAY DIFFRACTIONr_scbond_it2.7111.9821025
X-RAY DIFFRACTIONr_scbond_other2.6821.9711022
X-RAY DIFFRACTIONr_scangle_it4.1482.8371467
X-RAY DIFFRACTIONr_scangle_other4.1392.821462
X-RAY DIFFRACTIONr_lrange_it5.96720.5762136
X-RAY DIFFRACTIONr_lrange_other5.7619.8552086
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.458-1.4960.49480.251236X-RAY DIFFRACTION8.3935
1.496-1.5360.35490.2641042X-RAY DIFFRACTION38.5104
1.536-1.5810.277870.2541919X-RAY DIFFRACTION73.4799
1.581-1.630.2461310.2372416X-RAY DIFFRACTION94.8603
1.63-1.6830.2631080.2252474X-RAY DIFFRACTION99.9226
1.683-1.7420.2531230.2142394X-RAY DIFFRACTION100
1.742-1.8080.2181330.1932286X-RAY DIFFRACTION100
1.808-1.8820.2291090.1792225X-RAY DIFFRACTION100
1.882-1.9650.189980.1622156X-RAY DIFFRACTION100
1.965-2.0610.1831110.1522044X-RAY DIFFRACTION100
2.061-2.1720.186940.1461954X-RAY DIFFRACTION100
2.172-2.3040.1911110.1481836X-RAY DIFFRACTION100
2.304-2.4630.1721130.1541720X-RAY DIFFRACTION100
2.463-2.660.17860.1491625X-RAY DIFFRACTION100
2.66-2.9140.171790.1441515X-RAY DIFFRACTION100
2.914-3.2570.194690.151383X-RAY DIFFRACTION100
3.257-3.760.18520.1541224X-RAY DIFFRACTION100
3.76-4.6020.158600.1571049X-RAY DIFFRACTION100
4.602-6.4970.281390.207835X-RAY DIFFRACTION100
6.497-53.6910.241120.256511X-RAY DIFFRACTION99.8092

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