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: 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 ...

    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.


    Related Citations: 
    • Location of Iron and Sulfur Atoms in Myohemerythrin from Anomalous-Scattering Measurements
      Sheriff, S., Hendrickson, W.A.
      (1987) Acta Crystallogr B 43: 209
    • General Density Function Corresponding to X-Ray Diffraction with Anomalous Scattering Included
      Hendrickson, W.A., Sheriff, S.
      (1987) Acta Crystallogr A 43: 121
    • Description of Overall Anisotropy in Diffraction from Macromolecular Crystals
      Sheriff, S., Hendrickson, W.A.
      (1987) Acta Crystallogr A 43: 118
    • Structural Heterogeneity in Protein Crystals
      Smith, J.L., Hendrickson, W.A., Honzatko, R.B., Sheriff, S.
      (1986) Biochemistry 25: 5018
    • Mobility and Heterogeneity in Protein Structure as Seen by Diffraction
      Hendrickson, W.A., Smith, J.L., Sheriff, S.
      (1986) Biomolecular Stereodynamics Iii Proceedings Of The Fourth Conversation In The Discipline Of Biomolecular Stereodynamics --: 217
    • Influence of Solvent Accessibility and Intermolecular Contacts on Atomic Mobilities in Hemerythrins
      Sheriff, S., Hendrickson, W.A., Stenkamp, R.E., Sieker, L.C., Jensen, L.H.
      (1985) Proc Natl Acad Sci U S A 82: 1104
    • Structure and Function of Hemerythrins
      Hendrickson, W.A., Smith, J.L., Sheriff, S.
      (1985) Respiratory Pigments In Animals --: 1
    • Structure of the Active Center of Hemerythrins
      Sheriff, S., Hendrickson, W.A., Smith, J.L.
      (1983) Life Chem Rep ,suppl Ser 1: 305
    • Tertiary Structure of Myohemerythrin at Low Resolution
      Hendrickson, W.A., Klippenstein, G.L., Ward, K.B.
      (1975) Proc Natl Acad Sci U S A 72: 2160

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
MYOHEMERYTHRINA118Themiste hennahiMutation(s): 0 
UniProt
Find proteins for P02247 (Themiste hennahi)
Explore P02247 
Go to UniProtKB:  P02247
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FEO
Query on FEO

Download Ideal Coordinates CCD File 
F [auth A]MU-OXO-DIIRON
Fe2 O
NPMYUMBHPJGBFA-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A], D [auth A], E [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
AZI
Query on AZI

Download Ideal Coordinates CCD File 
B [auth A]AZIDE ION
N3
IVRMZWNICZWHMI-UHFFFAOYSA-N
 Ligand Interaction
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