9IKA | pdb_00009ika

Crystal structure of the tetrapyrrole binding domain in CoaR

• PDB DOI: https://doi.org/10.2210/pdb9IKA/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Synechocystis sp. PCC 6803 substr. Kazusa
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-06-26 Released: 2025-07-02 
• Deposition Author(s): Liu, X.C.
• Funding Organization(s): National Science Foundation (NSF, China)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.26 Å
• R-Value Free: 
  0.210 (Depositor), 0.213 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.201 (DCC) 

Starting Model: in silico

Literature

Crystal structure of the tetrapyrrole binding domain in CoaR

Liu, X.C.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 46.7 kDa 
• Atom Count: 2,770 
• Modeled Residue Count: 358 
• Deposited Residue Count: 436 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mercuric resistance operon regulatory protein precorrin isomerase	A, B	218	Synechocystis sp. PCC 6803 substr. Kazusa	Mutation(s): 0  Gene Names: merR
UniProt
Find proteins for Q55938 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa)) Explore Q55938  Go to UniProtKB:  Q55938

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	D [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL	C [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.26 Å
• R-Value Free:  0.210 (Depositor), 0.213 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.201 (DCC) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.365	α = 90
b = 101.5	β = 90
c = 48.653	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
DIALS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-07-02 
Deposition Author(s): Liu, X.C.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, China)	China	--

Revision History  

• Version 1.0: 2025-07-02
  Type: Initial release