8J4K

X-ray crystal structure of F46C myoglobin with a covalently linked phenol group

• PDB DOI: https://doi.org/10.2210/pdb8J4K/pdb

• Classification: OXYGEN STORAGE
• Organism(s): Physeter macrocephalus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2023-04-20 Released: 2024-04-24 
• Deposition Author(s): Yuan, H., Lin, Y.W.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.46 Å
• R-Value Free: 
  0.200 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.150 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.152 (Depositor) 

Starting Model: experimental

Literature

X-ray crystal structure of F46C myoglobin with a covalently linked phenol group

Yuan, H., Lin, Y.W.

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

Macromolecule Content

• Total Structure Weight: 18.13 kDa 
• Atom Count: 1,530 
• Modelled Residue Count: 153 
• 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	B [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
9UU (Subject of Investigation/LOI)	C [auth A]	1-(4-hydroxyphenyl)pyrrole-2,5-dione C10 H7 N O3 BLLFPKZTBLMEFG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.46 Å
• R-Value Free:  0.200 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.150 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.152 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.719	α = 90
b = 48.172	β = 90
c = 78.906	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-04-24 
Deposition Author(s): Yuan, H., Lin, Y.W.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2024-04-24
  Type: Initial release