2MHR

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å

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


  • 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 s ...

    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: 
    • General Density Function Corresponding to X-Ray Diffraction with Anomalous Scattering Included
      Hendrickson, W.A.,Sheriff, S.
      (1987) Acta Crystallogr.,Sect.A 43: 121
    • Tertiary Structure of Myohemerythrin at Low Resolution
      Hendrickson, W.A.,Klippenstein, G.L.,Ward, K.B.
      (1975) Proc.Natl.Acad.Sci.USA 72: 2160
    • 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.USA 82: 1104
    • Structure and Function of Hemerythrins
      Hendrickson, W.A.,Smith, J.L.,Sheriff, S.
      (1985) Respiratory Pigments in Animals --: 1
    • Structural Heterogeneity in Protein Crystals
      Smith, J.L.,Hendrickson, W.A.,Honzatko, R.B.,Sheriff, S.
      (1986) Biochemistry 25: 5018
    • Location of Iron and Sulfur Atoms in Myohemerythrin from Anomalous-Scattering Measurements
      Sheriff, S.,Hendrickson, W.A.
      (1987) Acta Crystallogr.,Sect.B 43: 209
    • 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
    • Description of Overall Anisotropy in Diffraction from Macromolecular Crystals
      Sheriff, S.,Hendrickson, W.A.
      (1987) Acta Crystallogr.,Sect.A 43: 118
    • Structure of the Active Center of Hemerythrins
      Sheriff, S.,Hendrickson, W.A.,Smith, J.L.
      (1983) Life Chem.Rep.,Suppl.Ser. 1: 305


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MYOHEMERYTHRIN
A
118Themiste hennahiMutation(s): 0 
Find proteins for P02247 (Themiste hennahi)
Go to UniProtKB:  P02247
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
AZI
Query on AZI

Download SDF File 
Download CCD File 
A
AZIDE ION
N3
IVRMZWNICZWHMI-UHFFFAOYSA-N
 Ligand Interaction
FEO
Query on FEO

Download SDF File 
Download CCD File 
A
MU-OXO-DIIRON
Fe2 O
NPMYUMBHPJGBFA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 41.660α = 90.00
b = 80.170β = 90.00
c = 37.820γ = 90.00
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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