1DWS

PHOTOLYZED CARBONMONOXY MYOGLOBIN (HORSE HEART)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

Crystal Structure of a New Ligand Binding Intermediate in Wildtype Carbonmonoxy Myoglobin

Chu, K., Vojtechovsky, J., Mcmahon, B.H., Sweet, R.M., Berendzen, J., Schlichting, I.

(2000) Nature 403: 921

  • DOI: 10.1038/35002641
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Small molecules such as NO, O2, CO or H2 are important biological ligands that bind to metalloproteins to function crucially in processes such as signal transduction, respiration and catalysis. A key issue for understanding the regulation of reaction ...

    Small molecules such as NO, O2, CO or H2 are important biological ligands that bind to metalloproteins to function crucially in processes such as signal transduction, respiration and catalysis. A key issue for understanding the regulation of reaction mechanisms in these systems is whether ligands gain access to the binding sites through specific channels and docking sites, or by random diffusion through the protein matrix. A model system for studying this issue is myoglobin, a simple haem protein. Myoglobin has been studied extensively by spectroscopy, crystallography, computation and theory. It serves as an aid to oxygen diffusion but also binds carbon monoxide, a byproduct of endogenous haem catabolism. Molecular dynamics simulations, random mutagenesis and flash photolysis studies indicate that ligand migration occurs through a limited number of pathways involving docking sites. Here we report the 1.4 A resolution crystal structure of a ligand-binding intermediate in carbonmonoxy myoglobin that may have far-reaching implications for understanding the dynamics of ligand binding and catalysis.

    Related Citations: 
    • A Myoglobin Variant with a Polar Substitution in a Conserved Hydrophobic Cluster in the Heme Binding Pocket
      Maurus, R.,Overall, C.M.,Bogumil, R.,Luo, Y.,Mauk, A.G.,Smith, M.,Brayer, G.D.
      (1997) Biochim.Biophys.Acta 1341: 1
    • Crystallization and Preliminary Diffraction Data for Horse Heart Metmyoglobin
      Sherwood, C.,Mauk, A.G.,Brayer, G.D.
      (1987) J.Mol.Biol. 193: 227
    • Crystal Structure of Photolysed Myoglobin
      Schlichting, I.,Berendzen, J.,Phillips Jr, G.N.,Sweet, R.M.
      (1994) Nature 371: 808

    Organizational Affiliation: 

    P-21 Biophysics Group, Los Alamos National Laboratory, New Mexico, 87545, USA. kelvin.chu@uvm.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MYOGLOBIN
A
153Equus caballusMutation(s): 0 
Gene Names: MB
Find proteins for P68082 (Equus caballus)
Go to Gene View: MB
Go to UniProtKB:  P68082
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
HEM
Query on HEM
Download SDF File 
Download CCD File 
A
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
CMO
Query on CMO
Download SDF File 
Download CCD File 
A
CARBON MONOXIDE
C O
UGFAIRIUMAVXCW-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.204 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 63.300α = 90.00
b = 28.800β = 106.70
c = 35.500γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-03-03
    Type: Initial release
  • Version 1.1: 2011-05-07
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance