1DM1

2.0 A CRYSTAL STRUCTURE OF THE DOUBLE MUTANT H(E7)V, T(E10)R OF MYOGLOBIN FROM APLYSIA LIMACINA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.189 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Engineering His(E7) affects the control of heme reactivity in Aplysia limacina myoglobin.

Federici, L.Savino, C.Musto, R.Travaglini-Allocatelli, C.Cutruzzola, F.Brunori, M.

(2000) Biochem Biophys Res Commun 269: 58-63

  • DOI: https://doi.org/10.1006/bbrc.2000.2259
  • Primary Citation of Related Structures:  
    1DM1

  • PubMed Abstract: 

    Aplysia limacina myoglobin lacks the distal histidine (His (E7)) and displays a ligand stabilization mechanism based on Arg(E10). The double mutant Val(E7)His-Arg(E10)Thr has been prepared to engineer the role of His(E7), typical of mammalian myoglobins, in a different globin framework. The 2.0 A crystal structure of Val(E7)His-Arg(E10)Thr met-Mb mutant reveals that the His(E7) side chain points out of the distal pocket, providing an explanation for the observed failure to stabilize the Fe(II) bound oxygen in the ferrous myoglobin. Moreover, spectroscopic analysis together with kinetic data on azide binding to met-myoglobin are reported and discussed in terms of the presence of a water molecule at coordination distance from the heme iron.


  • Organizational Affiliation

    Department of Biochemical Sciences "A. Rossi Fanelli" and C.N.R. Center for Molecular Biology, University of Rome "La Sapienza", Piazzale Aldo Moro 5, Rome, 00185, Italy.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
MYOGLOBIN146Aplysia limacinaMutation(s): 2 
UniProt
Find proteins for P02210 (Aplysia limacina)
Explore P02210 
Go to UniProtKB:  P02210
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02210
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
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: 1.99 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.189 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.73α = 90
b = 89.73β = 90
c = 92.08γ = 120
Software Package:
Software NamePurpose
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-06-21
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2021-11-03
    Changes: Database references, Derived calculations
  • Version 1.4: 2024-02-07
    Changes: Data collection