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- PDB-7qli: Cis structure of rsKiiro at 290 K -

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Basic information

Entry
Database: PDB / ID: 7qli
TitleCis structure of rsKiiro 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: 1.155 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.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 / citation_author
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 / _citation_author.identifier_ORCID

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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)25,5335
Polymers25,1521
Non-polymers3804
Water4,179232
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)38.560, 73.467, 78.038
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.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / 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: 2.22 Å3/Da / Density % sol: 44.52 %
Crystal growTemperature: 293 K / Method: batch mode
Details: 0.2 M LITHIUM SULFATE 0.1 M TRIS-CL PH 8.5 23-30% 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 EIGER X 16M / 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: 1.155→53.549 Å / Num. obs: 59836 / % possible obs: 77 % / Redundancy: 13.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.122 / Rrim(I) all: 0.127 / Net I/σ(I): 12.1
Reflection shellResolution: 1.159→1.261 Å / Num. unique obs: 2992 / CC1/2: 0.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
autoPROC1.0.5 (20180515)data reduction
STARANISO1.10.15data scaling
REFMAC5.8.0267phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5OQ9

5oq9


Resolution: 1.155→53.549 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.971 / WRfactor Rfree: 0.17 / WRfactor Rwork: 0.151 / SU B: 0.78 / SU ML: 0.033 / Average fsc free: 0.927 / Average fsc work: 0.931 / Cross valid method: FREE R-VALUE / ESU R: 0.044 / ESU R Free: 0.045
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1787 2888 4.827 %
Rwork0.1609 56948 -
all0.162 --
obs-59836 76.168 %
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: 13.723 Å2
Baniso -1Baniso -2Baniso -3
1--0.001 Å20 Å20 Å2
2--0.087 Å2-0 Å2
3----0.086 Å2
Refinement stepCycle: LAST / Resolution: 1.155→53.549 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1747 0 21 232 2000
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0132042
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161856
X-RAY DIFFRACTIONr_angle_refined_deg1.8111.6812783
X-RAY DIFFRACTIONr_angle_other_deg1.5271.6074322
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.515263
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.65323.304112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.06815359
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5131510
X-RAY DIFFRACTIONr_chiral_restr0.0960.2244
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022425
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02488
X-RAY DIFFRACTIONr_nbd_refined0.2870.2344
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2070.21717
X-RAY DIFFRACTIONr_nbtor_refined0.1760.2867
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0870.2973
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1950.2151
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0870.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0710.27
X-RAY DIFFRACTIONr_nbd_other0.1780.238
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1130.225
X-RAY DIFFRACTIONr_mcbond_it1.1871.176980
X-RAY DIFFRACTIONr_mcbond_other1.1741.172979
X-RAY DIFFRACTIONr_mcangle_it1.8471.7571261
X-RAY DIFFRACTIONr_mcangle_other1.8521.761262
X-RAY DIFFRACTIONr_scbond_it2.3471.4321062
X-RAY DIFFRACTIONr_scbond_other2.3491.4231051
X-RAY DIFFRACTIONr_scangle_it3.5312.0441520
X-RAY DIFFRACTIONr_scangle_other3.5372.0251503
X-RAY DIFFRACTIONr_lrange_it4.95314.5622204
X-RAY DIFFRACTIONr_lrange_other4.77314.0232160
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.155-1.1850.339110.282227X-RAY DIFFRACTION4.1377
1.185-1.2170.279390.282663X-RAY DIFFRACTION12.5852
1.217-1.2520.286800.2721510X-RAY DIFFRACTION29.1262
1.252-1.2910.2671320.2652411X-RAY DIFFRACTION47.9359
1.291-1.3330.2631650.2583556X-RAY DIFFRACTION72.7326
1.333-1.380.2452250.2474455X-RAY DIFFRACTION94.0325
1.38-1.4320.2332430.2264542X-RAY DIFFRACTION99.8331
1.432-1.4910.1942120.2064404X-RAY DIFFRACTION100
1.491-1.5570.1972440.1844195X-RAY DIFFRACTION100
1.557-1.6330.21800.1614081X-RAY DIFFRACTION100
1.633-1.7210.1741930.1473851X-RAY DIFFRACTION100
1.721-1.8260.1821660.1453682X-RAY DIFFRACTION100
1.826-1.9520.1651670.1393451X-RAY DIFFRACTION100
1.952-2.1080.1671530.1333249X-RAY DIFFRACTION100
2.108-2.3090.1621370.1332973X-RAY DIFFRACTION100
2.309-2.5810.1721510.142696X-RAY DIFFRACTION100
2.581-2.980.1721380.1452394X-RAY DIFFRACTION100
2.98-3.6480.1591270.1442017X-RAY DIFFRACTION100
3.648-5.1540.135900.1361616X-RAY DIFFRACTION100
5.154-53.5490.219350.208975X-RAY DIFFRACTION99.9011

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