6JP1

An X-ray structure of met sperm whale F43Y/T67R myoglobin with Tyr-heme double cross-links

• PDB DOI: https://doi.org/10.2210/pdb6JP1/pdb

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


• Deposited: 2019-03-25 Released: 2019-05-29 
• Deposition Author(s): Lin, Y.W., Yuan, H.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free: 
  0.220 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.171 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.173 (Depositor) 

Starting Model: experimental

Literature

Unique Tyr-heme double cross-links in F43Y/T67R myoglobin: an artificial enzyme with a peroxidase activity comparable to that of native peroxidases.

Liu, C., Yuan, H., Liao, F., Wei, C.W., Du, K.J., Gao, S.Q., Tan, X., Lin, Y.W.

(2019) Chem Commun (Camb) 55: 6610-6613

• PubMed: 31119219 
• DOI: https://doi.org/10.1039/c9cc02714a
• Primary Citation of Related Structures:  
  6JP1


• PubMed Abstract: 
  

  The X-ray crystal structure of F43Y/T67R myoglobin revealed unique Tyr-heme double cross-links between Tyr43 and the heme 4-vinyl group, which represents a novel post-translational modification of heme proteins. Moreover, with the feature of a distal His-Arg pair, the designed artificial enzyme exhibited a peroxidase activity comparable to that of native peroxidases, such as the most efficient horseradish peroxidase.

---

Organizational Affiliation: 

School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China. [e-mail] [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 35.48 kDa 
• Atom Count: 2,721 
• Modelled Residue Count: 302 
• Deposited Residue Count: 302 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Myoglobin	A, B	151	Physeter macrocephalus	Mutation(s): 2  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 (Subject of Investigation/LOI)	C [auth A], D [auth B]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free:  0.220 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.171 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.173 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.406	α = 90
b = 33.604	β = 117.87
c = 72.886	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-05-29 
Deposition Author(s): Lin, Y.W., Yuan, H.

Revision History  

• Version 1.0: 2019-05-29
  Type: Initial release
  
• Version 1.1: 2019-06-19
  Changes: Data collection, Database references
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Derived calculations, Refinement description