9R84 | pdb_00009r84

The C103F Mutant of Apo-C-Terminal Domain Homolog of the Orange Carotenoid Protein (CTDH) from Anabaena

• PDB DOI: https://doi.org/10.2210/pdb9R84/pdb

• Classification: PHOTOSYNTHESIS
• Organism(s): Cyanobacteriota
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2025-05-15 Released: 2025-08-06 
• Deposition Author(s): Sklyar, J., Adir, N.
• Funding Organization(s): Israel Science Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.260 (Depositor), 0.268 (DCC) 
• R-Value Work: 
  0.235 (Depositor), 0.246 (DCC) 
• R-Value Observed: 
  0.236 (Depositor) 

Starting Model: experimental

Literature

Structural Characterization of Carotenoid Binding Proteins in Cyanobacteria and Elucidation of Their Role in Carotenoid Uptake and Transfer Mechanism for Photoprotection

Sklyar, J.

(2025) Thesis 

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 28.2 kDa 
• Atom Count: 2,053 
• Modeled Residue Count: 252 
• Deposited Residue Count: 259 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
All4940 protein	A	129	Cyanobacteriota	Mutation(s): 1  Gene Names: all4940
UniProt
Find proteins for A0ACD6B996 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576)) Explore A0ACD6B996  Go to UniProtKB:  A0ACD6B996

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
All4940 protein	B	130	Cyanobacteriota	Mutation(s): 1  Gene Names: all4940
UniProt
Find proteins for A0ACD6B996 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576)) Explore A0ACD6B996  Go to UniProtKB:  A0ACD6B996

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FLC	D [auth B]	CITRATE ANION C6 H5 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-K
MLT	C [auth A], E [auth B]	D-MALATE C4 H6 O5 BJEPYKJPYRNKOW-UWTATZPHSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.260 (Depositor), 0.268 (DCC) 
• R-Value Work:  0.235 (Depositor), 0.246 (DCC) 
• R-Value Observed: 0.236 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.532	α = 90
b = 63.914	β = 99.46
c = 48.565	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-08-06 
Deposition Author(s): Sklyar, J., Adir, N.

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Funding Organization	Location	Grant Number
Israel Science Foundation	Israel	1596/21

Revision History  

• Version 1.0: 2025-08-06
  Type: Initial release