4ZBL | pdb_00004zbl

Phototoxic fluorescent protein mKillerOrange

• PDB DOI: https://doi.org/10.2210/pdb4ZBL/pdb

• Classification: FLUORESCENT PROTEIN
• Organism(s): Hydrozoa
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2015-04-14 Released: 2015-12-23 
• Deposition Author(s): Pletnev, V.Z., Pletneva, N.V., Pletnev, S.V.
• Funding Organization(s): Russian Science Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.57 Å
• R-Value Free: 
  0.175 (Depositor), 0.181 (DCC) 
• R-Value Work: 
  0.144 (Depositor), 0.156 (DCC) 
• R-Value Observed: 
  0.146 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Phototoxic Orange Fluorescent Proteins with a Tryptophan-Based Chromophore.

Pletneva, N.V., Pletnev, V.Z., Sarkisyan, K.S., Gorbachev, D.A., Egorov, E.S., Mishin, A.S., Lukyanov, K.A., Dauter, Z., Pletnev, S.

(2015) PLoS One 10: e0145740-e0145740

• PubMed: 26699366 
• DOI: https://doi.org/10.1371/journal.pone.0145740
• Primary Citation Related Structures: 
  4ZBL, 4ZFS


• PubMed Abstract: 
  

  Phototoxic fluorescent proteins represent a sparse group of genetically encoded photosensitizers that could be used for precise light-induced inactivation of target proteins, DNA damage, and cell killing. Only two such GFP-based fluorescent proteins (FPs), KillerRed and its monomeric variant SuperNova, were described up to date. Here, we present a crystallographic study of their two orange successors, dimeric KillerOrange and monomeric mKillerOrange, at 1.81 and 1.57 Å resolution, respectively. They are the first orange-emitting protein photosensitizers with a tryptophan-based chromophore (Gln65-Trp66-Gly67). Same as their red progenitors, both orange photosensitizers have a water-filled channel connecting the chromophore to the β-barrel exterior and enabling transport of ROS. In both proteins, Trp66 of the chromophore adopts an unusual trans-cis conformation stabilized by H-bond with the nearby Gln159. This trans-cis conformation along with the water channel was shown to be a key structural feature providing bright orange emission and phototoxicity of both examined orange photosensitizers.

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Organizational Affiliation: 
• Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation.
Faculty of Biology, Moscow State University, Moscow, Russian Federation.
Nizhny Novgorod State Medical Academy, Nizhny Novgorod, Russian Federation.
Synchrotron Radiation Research Section, Macromolecular Crystallography Laboratory, National Cancer Institute, Argonne, Illinois, United States of America.
Leidos Biomedical Research, Inc., Basic Research Program, Argonne, Illinois, United States of America.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 27.46 kDa 
• Atom Count: 2,091 
• Modeled Residue Count: 226 
• Deposited Residue Count: 240 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
KillerOrange	A	240	Hydrozoa	Mutation(s): 1
UniProt
Find proteins for Q2TCH5 (Anthomedusae sp. DC-2005) Explore Q2TCH5  Go to UniProtKB:  Q2TCH5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CIT	B [auth A]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N
GOL	C [auth A], D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
4M9	A	L-PEPTIDE LINKING	C18 H17 N5 O4		GLN, TRP, GLY

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.57 Å
• R-Value Free:  0.175 (Depositor), 0.181 (DCC) 
• R-Value Work:  0.144 (Depositor), 0.156 (DCC) 
• R-Value Observed: 0.146 (Depositor) 

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.16	α = 90
b = 64.16	β = 90
c = 47.35	γ = 120

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data scaling
MOLREP	phasing
HKL-2000	data scaling

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2015-12-23 
Deposition Author(s): Pletnev, V.Z., Pletneva, N.V., Pletnev, S.V.

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Funding Organization	Location	Grant Number
Russian Science Foundation	Russian Federation	14-14-00281

Revision History  

• Version 1.0: 2015-12-23
  Type: Initial release
  
• Version 1.1: 2016-01-13
  Changes: Database references
• Version 1.2: 2017-11-29
  Changes: Database references
• Version 1.3: 2018-08-29
  Changes: Data collection, Database references
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Database references, Derived calculations
• Version 2.1: 2024-01-10
  Changes: Refinement description
• Version 3.0: 2024-05-15
  Changes: Database references, Derived calculations, Polymer sequence, Structure summary
• Version 4.0: 2024-07-10
  Changes: Data collection, Non-polymer description, Structure summary
• Version 4.1: 2024-11-06
  Changes: Structure summary
• Version 5.0: 2026-03-18
  Changes: Polymer sequence