8AFK | pdb_00008afk

Structure of iRFP variant C15S/N136R/V256C in complex with phycocyanobilin

• PDB DOI: https://doi.org/10.2210/pdb8AFK/pdb

• Classification: FLUORESCENT PROTEIN
• Organism(s): Rhodopseudomonas palustris CGA009
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2022-07-18 Released: 2023-08-16 
• Deposition Author(s): Remeeva, A., Kovalev, K., Gushchin, I., Fonin, A., Turoverov, K., Stepanenko, O.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.02 Å
• R-Value Free: 
  0.280 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.240 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.242 (Depositor) 

Literature

Structure of iRFP variant C15S/N136R/V256C in complex with phycocyanobilin

Remeeva, A., Kovalev, K., Gushchin, I., Fonin, A., Turoverov, K., Stepanenko, O.

To be published.

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: 70.52 kDa 
• Atom Count: 4,511 
• Modeled Residue Count: 565 
• Deposited Residue Count: 632 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Near-infrared fluorescent protein	A, B	316	Rhodopseudomonas palustris CGA009	Mutation(s): 3  Gene Names: iRFP
UniProt
Find proteins for G1FNL7 (Rhodopseudomonas palustris) Explore G1FNL7  Go to UniProtKB:  G1FNL7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CYC (Subject of Investigation/LOI)	C [auth A], D [auth B]	PHYCOCYANOBILIN C33 H40 N4 O6 VXTXPYZGDQPMHK-GMXXPEQVSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.02 Å
• R-Value Free:  0.280 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.240 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.242 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.806	α = 90
b = 98.708	β = 90
c = 156.833	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
STARANISO	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-08-16 
Deposition Author(s): Remeeva, A., Kovalev, K., Gushchin, I., Fonin, A., Turoverov, K., Stepanenko, O.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-08-16
  Type: Initial release
  
• Version 1.1: 2024-10-23
  Changes: Structure summary