1MYG

HIGH RESOLUTION X-RAY STRUCTURES OF PIG METMYOGLOBIN AND TWO CD3 MUTANTS MB(LYS45-> ARG) AND MB(LYS45-> SER)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Observed: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

High-resolution X-ray structures of pig metmyoglobin and two CD3 mutants: Mb(Lys45----Arg) and Mb(Lys45----Ser).

Oldfield, T.J.Smerdon, S.J.Dauter, Z.Petratos, K.Wilson, K.S.Wilkinson, A.J.

(1992) Biochemistry 31: 8732-8739

  • DOI: 10.1021/bi00152a008
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The structure of pig aquometmyoglobin has been refined to a crystallographic R-factor of 19.8% against X-ray diffraction data between 10- and 1.75-A spacing. The final structural model comprises two molecules of pig myoglobin, 233 water molecules, an ...

    The structure of pig aquometmyoglobin has been refined to a crystallographic R-factor of 19.8% against X-ray diffraction data between 10- and 1.75-A spacing. The final structural model comprises two molecules of pig myoglobin, 233 water molecules, and two sulfate ions. A water molecule is coordinated to each of the heme iron atoms with an average Fe-OH2 bond distance of 2.19 A, and the mean Fe-N epsilon (proximal histidine-93) distance is 2.20 A. In contrast to the structure of sperm whale metmyoglobin, the iron is not significantly displaced from the plane of the heme. At the entrance to the heme pocket, the side-chain amino group of lysine-45 (CD3) is well-defined in the electron density map and forms salt-bridging interactions with the heme 6-propionate and with a sulfate ion. Serine and arginine replacements have been made previously at position 45 to examine the proposal that the CD3 side chain acts as a barrier to ligand entry into the protein. Crystal structures of the arginine-45 and serine-45 mutant metmyoglobins have been solved to 1.9 and 2.0 A resolution, respectively. In both cases the structural changes are confined to the site of mutation. Arginine-45 takes up a conformation closely similar to that observed for this residue in wild-type sperm whale myoglobin, in which it makes more extensive charge-charge and charge-dipole interactions and appears to restrict the movement of the distal histidine away from the ligand. The hydroxyl group of serine-45 is disordered, but it is clear that the effect of the mutation is to open up the solvent-exposed face of the heme pocket.


    Related Citations: 
    • Distal Polarity in Ligand Binding to Myoglobin: Structural and Functional Characterization of a Threonine68(E11) Mutant
      Smerdon, S.J., Dodson, G.G., Wilkinson, A.J., Gibson, Q.H., Blackmore, R.S., Carver, T.E., Olson, J.S.
      (1991) Biochemistry 30: 6252
    • Determination of the Crystal Structure of Recombinant Pig Myoglobin by Molecular Replacement and its Refinement
      Smerdon, S.J., Oldfield, T.J., Dodson, E.J., Dodson, G.G., Hubbard, R.E., Wilkinson, A.J.
      (1990) Acta Crystallogr B 46: 370
    • Apomyoglobin as a Molecular Recognition Surface: Expression, Reconstitution and Crystallisation of Recombinant Porcine Myoglobin in Escherichia Coli
      Dodson, G.G., Hubbard, R.E., Oldfield, T.J., Smerdon, S.J., Wilkinson, A.J.
      (1988) Protein Eng 2: 233

    Organizational Affiliation

    Department of Chemistry, University of York, U.K.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MYOGLOBIN
A, B
153Sus scrofaMutation(s): 0 
Gene Names: MB
Find proteins for P02189 (Sus scrofa)
Go to UniProtKB:  P02189
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download CCD File 
A, B
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Observed: 0.198 
  • Space Group: I 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 125.26α = 90
b = 42.49β = 92.29
c = 92.37γ = 90
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1994-01-31
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance