2MHR

STRUCTURE OF MYOHEMERYTHRIN IN THE AZIDOMET STATE AT 1.7(SLASH)1.3 ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Observed: 0.158 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure of myohemerythrin in the azidomet state at 1.7/1.3 A resolution.

Sheriff, S.Hendrickson, W.A.Smith, J.L.

(1987) J Mol Biol 197: 273-296

  • DOI: https://doi.org/10.1016/0022-2836(87)90124-0
  • Primary Citation of Related Structures:  
    2MHR

  • PubMed Abstract: 

    The molecular model of myohemerythrin, an oxygen-carrying protein from sipunculan worms, has been refined by stereochemically restrained least-squares minimization at 1.7/1.3 A resolution to a conventional R-value of 0.158. The estimated positional standard deviation is better than 0.15 A for most of the 979 protein atoms. The average isotropic displacement parameter, B, for the protein atoms is 23.1 A2. This high average B parameter appears to be due to the overall motion of the molecule, which correlates with the observed anisotropic diffraction. The side-chains of seven residues were modeled in two conformations, i.e. the side-chains were discretely disordered, and B parameters for several lysine and glutamate side-chains indicate that they are poorly localized. Of the residues in myohemerythrin, 66% are helical, with 62% occurring in four long alpha-helices with mean values for the backbone torsion angles of phi = -65 degrees, psi = -42 degrees, and for the hydrogen bonds distances of N ... O, 3.0 A and H ... O, 2.1 A, and angles of N ... O = C, 153 degrees, N-H ... O, 157 degrees, and H ... O = C, 147 degrees. For two-thirds of the alpha-helical residues, the torsional rotation of the C alpha-C beta bond, chi 1, is approximately -60 degrees, and for one-third chi 1 is approximately 180 degrees. Although most turns in myohemerythrin are well-categorized by previous classification, two do not fit in established patterns. Also included in the refined model are three sulfate ions, all partially occupied, and 157 water molecules, 40% of which are modeled fully occupied. Only one water molecule is internal to the protein, the remainder occur on the surface and are observed principally between symmetry-related molecules contributing, along with van der Waals' contacts, most of the interactions between molecules. There are eight intermolecular protein-protein hydrogen bonds, of which only four are between well-located atoms.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
MYOHEMERYTHRIN118Themiste hennahiMutation(s): 0 
UniProt
Find proteins for P02247 (Themiste hennahi)
Explore P02247 
Go to UniProtKB:  P02247
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02247
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Observed: 0.158 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.66α = 90
b = 80.17β = 90
c = 37.82γ = 90
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1987-10-16
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-11-29
    Changes: Derived calculations, Other