9IJO | pdb_00009ijo

X-ray crystal structure of F46C myoglobin with a covalently linked 4-methyl-2,2'-bipyridine group in complex with Cu2+

• PDB DOI: https://doi.org/10.2210/pdb9IJO/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Physeter macrocephalus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2024-06-25 Released: 2025-07-02 
• Deposition Author(s): Lin, Y.W.
• Funding Organization(s): National Science Foundation (NSF, China)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.53 Å
• R-Value Free: 
  0.194 (Depositor), 0.194 (DCC) 
• R-Value Work: 
  0.167 (Depositor), 0.168 (DCC) 
• R-Value Observed: 
  0.169 (Depositor) 

Starting Model: experimental

Literature

X-ray crystal structure of F46C myoglobin with a covalently linked 4-methyl-2,2'-bipyridine group in complex with Cu2+

Lin, Y.W.

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: mass spectrometry

Macromolecule Content 

• Total Structure Weight: 18.19 kDa 
• Atom Count: 1,463 
• Modeled Residue Count: 152 
• Deposited Residue Count: 154 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Myoglobin	A	154	Physeter macrocephalus	Mutation(s): 1  Gene Names: MB EC: 1.11.1 (UniProt), 1.7 (UniProt)
UniProt
Find proteins for P02185 (Physeter macrocephalus) Explore P02185  Go to UniProtKB:  P02185

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM (Subject of Investigation/LOI)	B [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
A1D9G (Subject of Investigation/LOI)	C [auth A]	4-methyl-2-(4-methylpyridin-2-yl)pyridine C12 H12 N2 NBPGPQJFYXNFKN-UHFFFAOYSA-N
CU	D [auth A]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.53 Å
• R-Value Free:  0.194 (Depositor), 0.194 (DCC) 
• R-Value Work:  0.167 (Depositor), 0.168 (DCC) 
• R-Value Observed: 0.169 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.989	α = 90
b = 77.523	β = 90
c = 39.751	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	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): Lin, Y.W.

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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