8GOS | pdb_00008gos

Crystal structure of fluorescent protein RasM

• PDB DOI: https://doi.org/10.2210/pdb8GOS/pdb

• Classification: FLUORESCENT PROTEIN
• Organism(s): Discosoma sp.
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-08-25 Released: 2023-09-27 
• Deposition Author(s): Adachi, M., Kagotani, Y., Shimizu, R.
• Funding Organization(s): Ministry of Education, Culture, Sports, Science and Technology (Japan)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.01 Å
• R-Value Free: 
  0.158 (Depositor), 0.159 (DCC) 
• R-Value Work: 
  0.138 (Depositor), 0.139 (DCC) 
• R-Value Observed: 
  0.139 (Depositor) 

Literature

Beat-frequency-resolved two-dimensional electronic spectroscopy: disentangling vibrational coherences in artificial fluorescent proteins with sub-10-fs visible laser pulses.

Tsubouchi, M., Ishii, N., Kagotani, Y., Shimizu, R., Fujita, T., Adachi, M., Itakura, R.

(2023) Opt Express 31: 6890-6906

• PubMed: 36823935 
• DOI: https://doi.org/10.1364/OE.480505
• Primary Citation Related Structures: 
  8GOS


• PubMed Abstract: 
  

  We perform a beat-frequency-resolved analysis for two-dimensional electronic spectroscopy using a high-speed and stable 2D electronic spectrometer and few-cycle visible laser pulses to disentangle the vibrational coherences in an artificial fluorescent protein. We develop a highly stable ultrashort light source that generates 5.3-fs visible pulses with a pulse energy of 4.7 µJ at a repetition rate of 10 kHz using multi-plate pulse compression and laser filamentation in a gas cell. The above-5.3-fs laser pulses together with a high-speed multichannel detector enable us to measure a series of 2D electronic spectra, which are resolved in terms of beat frequency related to vibrational coherence. We successfully extract the discrete vibrational peaks behind the inhomogeneous broadening in the absorption spectra and the vibrational quantum beats of the excited electronic state behind the strong incoherent population background in the typical 2D electronic spectra.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 51.63 kDa 
• Atom Count: 4,129 
• Modeled Residue Count: 430 
• Deposited Residue Count: 452 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RasM	A, B	226	Discosoma sp.	Mutation(s): 0
UniProt
Find proteins for D0VWW2 (Discosoma sp.) Explore D0VWW2  Go to UniProtKB:  D0VWW2

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
NRQ	A, B	L-PEPTIDE LINKING	C16 H17 N3 O4 S		MET, TYR, GLY

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.01 Å
• R-Value Free:  0.158 (Depositor), 0.159 (DCC) 
• R-Value Work:  0.138 (Depositor), 0.139 (DCC) 
• R-Value Observed: 0.139 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.394	α = 90
b = 62.328	β = 90
c = 107.819	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
pointless	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-09-27 
Deposition Author(s): Adachi, M., Kagotani, Y., Shimizu, R.

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Funding Organization	Location	Grant Number
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	JPMXS0120330644

Revision History  

• Version 1.0: 2023-09-27
  Type: Initial release
  
• Version 1.1: 2023-11-15
  Changes: Data collection
• Version 2.0: 2026-03-18
  Changes: Polymer sequence, Structure summary