7LG4 | pdb_00007lg4

Green fluorescent protein from Aequorea macrodactyla - amacGFP

• PDB DOI: https://doi.org/10.2210/pdb7LG4/pdb

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


• Deposited: 2021-01-19 Released: 2021-01-27 
• Deposition Author(s): Bozhanova, N.G., Meiler, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.81 Å
• R-Value Free: 
  0.228 (Depositor), 0.239 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.193 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Starting Model: experimental

Literature

Heterogeneity of the GFP fitness landscape and data-driven protein design.

Gonzalez Somermeyer, L., Fleiss, A., Mishin, A.S., Bozhanova, N.G., Igolkina, A.A., Meiler, J., Alaball Pujol, M.E., Putintseva, E.V., Sarkisyan, K.S., Kondrashov, F.A.

(2022) Elife 11

• PubMed: 35510622 
• DOI: https://doi.org/10.7554/eLife.75842
• Primary Citation Related Structures: 
  7LG4


• PubMed Abstract: 
  

  Studies of protein fitness landscapes reveal biophysical constraints guiding protein evolution and empower prediction of functional proteins. However, generalisation of these findings is limited due to scarceness of systematic data on fitness landscapes of proteins with a defined evolutionary relationship. We characterized the fitness peaks of four orthologous fluorescent proteins with a broad range of sequence divergence. While two of the four studied fitness peaks were sharp, the other two were considerably flatter, being almost entirely free of epistatic interactions. Mutationally robust proteins, characterized by a flat fitness peak, were not optimal templates for machine-learning-driven protein design - instead, predictions were more accurate for fragile proteins with epistatic landscapes. Our work paves insights for practical application of fitness landscape heterogeneity in protein engineering.

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Organizational Affiliation: 
• Institute of Science and Technology Austria, Klosterneuburg, Austria.
Synthetic Biology Group, MRC London Institute of Medical Sciences, London, United Kingdom.
Institute of Clinical Sciences, Faculty of Medicine and Imperial College Centre for Synthetic Biology, Imperial College London, London, United Kingdom.
Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation.
Department of Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, United States.
Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria.
Institute for Drug Discovery, Medical School, Leipzig University, Leipzig, Germany.
LabGenius, London, United Kingdom.
Evolutionary and Synthetic Biology Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan.

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: 28.36 kDa 
• Atom Count: 2,051 
• Modeled Residue Count: 228 
• Deposited Residue Count: 242 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Green fluorescent protein	A	242	Aequorea macrodactyla	Mutation(s): 1  Gene Names: GFP
UniProt
Find proteins for Q8WTC7 (Aequorea macrodactyla) Explore Q8WTC7  Go to UniProtKB:  Q8WTC7

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	G [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL	H [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
GYS	A	L-PEPTIDE LINKING	C14 H15 N3 O5		SER, TYR, GLY

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.81 Å
• R-Value Free:  0.228 (Depositor), 0.239 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.193 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.089	α = 90
b = 47.488	β = 102.01
c = 69.294	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOLREP	phasing
PROTEUM PLUS	data scaling
PDB_EXTRACT	data extraction
PROTEUM PLUS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-01-27 
Deposition Author(s): Bozhanova, N.G., Meiler, J.

Revision History  

• Version 1.0: 2021-01-27
  Type: Initial release
  
• Version 1.1: 2022-05-11
  Changes: Database references
• Version 1.2: 2022-05-18
  Changes: Database references
• Version 1.3: 2023-10-18
  Changes: Data collection, Refinement description
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Derived calculations
• Version 2.1: 2024-11-20
  Changes: Structure summary
• Version 3.0: 2026-03-18
  Changes: Polymer sequence