7QLL | pdb_00007qll

rsKiiro Thermal annealing at 290K of 200K Cis intermediate

• PDB DOI: https://doi.org/10.2210/pdb7QLL/pdb

• Classification: FLUORESCENT PROTEIN
• Organism(s): Lobophyllia hemprichii
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2021-12-20 Released: 2023-07-05 
• Deposition Author(s): van Thor, J.J., Baxter, J.M.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.32 Å
• R-Value Free: 
  0.198 (Depositor), 0.197 (DCC) 
• R-Value Work: 
  0.170 (Depositor), 0.169 (DCC) 

Starting Model: experimental

Literature

Optical control of ultrafast structural dynamics in a fluorescent protein.

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.

(2023) Nat Chem 15: 1607-1615

• PubMed: 37563326 
• DOI: https://doi.org/10.1038/s41557-023-01275-1
• Primary Citation Related Structures: 
  7QLI, 7QLJ, 7QLK, 7QLL, 7QLM, 7QLN, 7QLO


• PubMed Abstract: 
  

  The photoisomerization reaction of a fluorescent protein chromophore occurs on the ultrafast timescale. The structural dynamics that result from femtosecond optical excitation have contributions from vibrational and electronic processes and from reaction dynamics that involve the crossing through a conical intersection. The creation and progression of the ultrafast structural dynamics strongly depends on optical and molecular parameters. When using X-ray crystallography as a probe of ultrafast dynamics, the origin of the observed nuclear motions is not known. Now, high-resolution pump-probe X-ray crystallography reveals complex sub-ångström, ultrafast motions and hydrogen-bonding rearrangements in the active site of a fluorescent protein. However, we demonstrate that the measured motions are not part of the photoisomerization reaction but instead arise from impulsively driven coherent vibrational processes in the electronic ground state. A coherent-control experiment using a two-colour and two-pulse optical excitation strongly amplifies the X-ray crystallographic difference density, while it fully depletes the photoisomerization process. A coherent control mechanism was tested and confirmed the wave packets assignment.

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Organizational Affiliation: 
• Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, UK.
Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK.
Quantum Optics and Laser Science Group, Blackett Laboratory, Imperial College London, London, UK.
Department of Chemistry, Stanford University, Stanford, CA, USA.
Physics Department, University of Wisconsin-Milwaukee, Milwaukee, WI, USA.
Physikalisch Chemisches Institut, Ruprecht-Karls Universität Heidelberg, Heidelberg, Germany.
Nanoscience Center and Department of Chemistry, University of Jyväskylä, Jyväskylä, Finland.
Pohang Accelerator Laboratory, POSTECH, Pohang, Republic of Korea.
Department of Chemical Engineering, POSTECH, Pohang, Republic of Korea.
RIKEN SPring-8 Center, Sayo, Hyogo, Japan.
Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai, Miyagi, Japan.
Department of Cell Biology, Graduate School of Medicine, Kyoto University, Sakyo, Kyoto, Japan.
Japan Synchrotron Radiation Research Institute, Sayo, Hyogo, Japan.
Linac Coherent Light Source, Stanford Linear Accelerator Centre (SLAC), National Accelerator Laboratory, Menlo Park, CA, USA.
Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Hamburg, Germany.
Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, UK. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 25.34 kDa 
• Atom Count: 2,091 
• Modeled Residue Count: 219 
• Deposited Residue Count: 220 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
rsKiiro	A	220	Lobophyllia hemprichii	Mutation(s): 12
UniProt
Find proteins for Q5S6Z9 (Lobophyllia hemprichii) Explore Q5S6Z9  Go to UniProtKB:  Q5S6Z9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	B [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PIA	A	L-PEPTIDE LINKING	C14 H15 N3 O4		ALA, TYR, GLY

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.32 Å
• R-Value Free:  0.198 (Depositor), 0.197 (DCC) 
• R-Value Work:  0.170 (Depositor), 0.169 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.671	α = 90
b = 73.803	β = 90
c = 78.111	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
STARANISO	data scaling
REFMAC	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-07-05 
Deposition Author(s): van Thor, J.J., Baxter, J.M.

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Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/P00752X/1

Revision History  

• Version 1.0: 2023-07-05
  Type: Initial release
  
• Version 1.1: 2023-08-16
  Changes: Data collection, Database references
• Version 1.2: 2023-08-23
  Changes: Database references, Structure summary
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Database references