6JP1 | pdb_00006jp1

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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free: 
  0.220 (Depositor), 0.234 (DCC) 
• R-Value Work: 
  0.171 (Depositor), 0.186 (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 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.

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Organizational Affiliation: 
• School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China. [e-mail] [e-mail].
Department of Chemistry & Institute of Biomedical Science, Fudan University, Shanghai 200433, China.
Laboratory of Protein Structure and Function, University of South China, Hengyang 421001, China.
School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China. [e-mail] [e-mail] and Laboratory of Protein Structure and Function, University of South China, Hengyang 421001, China.

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 
• Modeled 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), 0.234 (DCC) 
• R-Value Work:  0.171 (Depositor), 0.186 (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