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- PDB-7qln: rsKiiro pump probe structure by TR-SFX -

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Basic information

Entry
Database: PDB / ID: 7qln
TitlersKiiro pump probe structure by TR-SFX
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 / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
Authorsvan Thor, J.J.
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 1.0Oct 18, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Refinement description / Category: refine / Item: _refine.details
Revision 1.2Nov 15, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...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

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Assembly

Deposited unit
A: rsKiiro


Theoretical massNumber of molelcules
Total (without water)25,1521
Polymers25,1521
Non-polymers00
Water2,900161
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area670 Å2
ΔGint-1 kcal/mol
Surface area10350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.340, 74.010, 78.620
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 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 2.28 Å3/Da / Density % sol: 45.94 %
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: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: CXI / Wavelength: 1.305 Å
DetectorType: CS-PAD CXI-1 / Detector: PIXEL / Date: Feb 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.305 Å / Relative weight: 1
ReflectionResolution: 1.31→19 Å / Num. obs: 51252 / % possible obs: 100 % / Redundancy: 157 % / Biso Wilson estimate: 19.87 Å2 / CC1/2: 0.99 / R split: 0.1219 / Net I/σ(I): 4.566
Reflection shellResolution: 1.31→1.34 Å / Num. unique obs: 172 / CC1/2: 0.05 / R split: 3.5
Serial crystallography sample deliveryMethod: injection

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.27data extraction
CrystFELdata reduction
CrystFELdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5OQE

5oqe


Resolution: 1.5→11.99 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.912 / SU B: 4.576 / SU ML: 0.15 / Cross valid method: THROUGHOUT / ESU R: 0.144 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; The model corresponds to 14 percentage of non-extrapolated structure factors.
RfactorNum. reflection% reflectionSelection details
Rfree0.36425 1863 5 %RANDOM
Rwork0.34243 ---
obs0.34352 35571 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å2-0 Å20 Å2
2--0.3 Å2-0 Å2
3----0.1 Å2
Refinement stepCycle: 1 / Resolution: 1.5→11.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1723 0 20 161 1904
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0131992
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171809
X-RAY DIFFRACTIONr_angle_refined_deg1.7331.6672731
X-RAY DIFFRACTIONr_angle_other_deg1.2971.5964257
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4975273
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.68822.696115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.63815361
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.1421512
X-RAY DIFFRACTIONr_chiral_restr0.0810.2252
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022307
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02445
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1441.49930
X-RAY DIFFRACTIONr_mcbond_other1.1431.49931
X-RAY DIFFRACTIONr_mcangle_it1.6882.2291176
X-RAY DIFFRACTIONr_mcangle_other1.6922.2331177
X-RAY DIFFRACTIONr_scbond_it1.5611.6891062
X-RAY DIFFRACTIONr_scbond_other1.5571.6881061
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.4182.4561526
X-RAY DIFFRACTIONr_long_range_B_refined6.16617.5452159
X-RAY DIFFRACTIONr_long_range_B_other5.8417.2232135
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.615 118 -
Rwork0.631 2592 -
obs--100 %

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