6JP1

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.171 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

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

  • DOI: 10.1039/c9cc02714a

  • 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 ...

    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

    Department of Chemistry & Institute of Biomedical Science, Fudan University, Shanghai 200433, China.,School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China. linlinying@hotmail.com ywlin@usc.edu.cn and Laboratory of Protein Structure and Function, University of South China, Hengyang 421001, 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. linlinying@hotmail.com ywlin@usc.edu.cn.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Myoglobin
A, B
151Physeter macrocephalusMutation(s): 2 
Gene Names: MB
Find proteins for P02185 (Physeter macrocephalus)
Go to Gene View: MB
Go to UniProtKB:  P02185
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download SDF File 
Download CCD File 
A, B
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.171 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 72.406α = 90.00
b = 33.604β = 117.87
c = 72.886γ = 90.00
Software Package:
Software NamePurpose
HKL-3000data reduction
HKL-3000data scaling
REFMACrefinement
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2019-03-25 
  • 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
    Type: Data collection, Database references