5CN5

Ultrafast dynamics in myoglobin: 0 ps time delay


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.175 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Direct observation of ultrafast collective motions in CO myoglobin upon ligand dissociation.

Barends, T.R.Foucar, L.Ardevol, A.Nass, K.Aquila, A.Botha, S.Doak, R.B.Falahati, K.Hartmann, E.Hilpert, M.Heinz, M.Hoffmann, M.C.Kofinger, J.Koglin, J.E.Kovacsova, G.Liang, M.Milathianaki, D.Lemke, H.T.Reinstein, J.Roome, C.M.Shoeman, R.L.Williams, G.J.Burghardt, I.Hummer, G.Boutet, S.Schlichting, I.

(2015) Science 350: 445-450

  • DOI: 10.1126/science.aac5492
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The hemoprotein myoglobin is a model system for the study of protein dynamics. We used time-resolved serial femtosecond crystallography at an x-ray free-electron laser to resolve the ultrafast structural changes in the carbonmonoxy myoglobin complex ...

    The hemoprotein myoglobin is a model system for the study of protein dynamics. We used time-resolved serial femtosecond crystallography at an x-ray free-electron laser to resolve the ultrafast structural changes in the carbonmonoxy myoglobin complex upon photolysis of the Fe-CO bond. Structural changes appear throughout the protein within 500 femtoseconds, with the C, F, and H helices moving away from the heme cofactor and the E and A helices moving toward it. These collective movements are predicted by hybrid quantum mechanics/molecular mechanics simulations. Together with the observed oscillations of residues contacting the heme, our calculations support the prediction that an immediate collective response of the protein occurs upon ligand dissociation, as a result of heme vibrational modes coupling to global modes of the protein.


    Organizational Affiliation

    Max-Planck-Institut für Medizinische Forschung, Jahnstraße 29, 69120 Heidelberg, Germany. thomas.barends@mpimf-heidelberg.mpg.de ilme.schlichting@mpimf-heidelberg.mpg.de.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Myoglobin
A
152Equus 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: 1.8 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.175 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 63.600α = 90.00
b = 28.800β = 106.50
c = 35.600γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
CrystFELdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2015-09-16
    Type: Initial release
  • Version 1.1: 2015-09-23
    Type: Database references
  • Version 1.2: 2015-11-04
    Type: Database references
  • Version 1.3: 2018-01-24
    Type: Data collection
  • Version 1.4: 2018-11-14
    Type: Data collection