4QAU

Crystal structure of F43Y mutant of sperm whale myoglobin

• PDB DOI: https://doi.org/10.2210/pdb4QAU/pdb

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


• Deposited: 2014-05-06 Released: 2015-01-21 
• Deposition Author(s): Lin, Y., Tan, X., Li, W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.204 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.177 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

Starting Model: experimental

Literature

A Novel Tyrosine-Heme C-O Covalent Linkage in F43Y Myoglobin: A New Post-translational Modification of Heme Proteins

Yan, D.-J., Li, W., Xiang, Y., Wen, G.-B., Lin, Y.-W., Tan, X.

(2015) Chembiochem 16: 47-50

• PubMed: 25392956 
• DOI: https://doi.org/10.1002/cbic.201402504
• Primary Citation of Related Structures:  
  4QAU


• PubMed Abstract: 
  

  Heme post-translational modification plays a key role in tuning the structure and function of heme proteins. We herein report a novel tyrosine-heme covalent C−O bond in an artificially produced sperm whale myoglobin (Mb) mutant, F43Y Mb, which formed spontaneously in vivo between the Tyr43 hydroxy group and the heme 4-vinyl group. This highlights the diverse chemistry of heme post-translational modifications, and lays groundwork for further investigation of the structural and functional diversity of covalently-bound heme proteins.

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Organizational Affiliation: 

School of Chemistry and Chemical Engineering, University of South China, Changsheng Road 28, Hengyang 421001 (China).

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 18 kDa 
• Atom Count: 1,465 
• 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 1 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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.204 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.177 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.871	α = 90
b = 48.4	β = 90
c = 78.787	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-01-21 
Deposition Author(s): Lin, Y., Tan, X., Li, W.

Revision History  

• Version 1.0: 2015-01-21
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description