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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.02 Å
R-Value Free:
0.280 (Depositor), 0.284 (DCC)
R-Value Work:
0.240 (Depositor), 0.232 (DCC)
R-Value Observed:
0.242 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

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.

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

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	G1FNL7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CYC (Subject of Investigation/LOI) Query on CYC Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	PHYCOCYANOBILIN C₃₃ H₄₀ N₄ O₆ VXTXPYZGDQPMHK-GMXXPEQVSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.02 Å
R-Value Free: 0.280 (Depositor), 0.284 (DCC)
R-Value Work: 0.240 (Depositor), 0.232 (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

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-08-16

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2023-08-16
Type: Initial release
Version 1.1: 2024-10-23
Changes: Structure summary
Version 1.2: 2026-03-04
Changes: Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.