1MZ0

STRUCTURE OF MYOGLOBIN MB-YQR 316 ns AFTER PHOTOLYSIS OF CARBON MONOXIDE SOLVED FROM LAUE DATA AT RT.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.150 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Complex landscape of protein structural dynamics unveiled by nanosecond Laue crystallography.

Bourgeois, D.Vallone, B.Schotte, F.Arcovito, A.Miele, A.E.Sciara, G.Wulff, M.Anfinrud, P.Brunori, M.

(2003) Proc.Natl.Acad.Sci.USA 100: 8704-8709

  • DOI: 10.1073/pnas.1430900100
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Although conformational changes are essential for the function of proteins, little is known about their structural dynamics at atomic level resolution. Myoglobin (Mb) is the paradigm to investigate conformational dynamics because it is a simple globu ...

    Although conformational changes are essential for the function of proteins, little is known about their structural dynamics at atomic level resolution. Myoglobin (Mb) is the paradigm to investigate conformational dynamics because it is a simple globular heme protein displaying a photosensitivity of the iron-ligand bond. Upon laser photodissociation of carboxymyoglobin Mb a nonequilibrium population of protein structures is generated that relaxes over a broad time range extending from picoseconds to milliseconds. This process is associated with migration of the ligand to cavities in the matrix and with a reduction in the geminate rebinding rate by several orders of magnitude. Here we report nanosecond time-resolved Laue diffraction data to 1.55-A resolution on a Mb mutant, which depicts the sequence of structural events associated with this extended relaxation. Motions of the distal E-helix, including the mutated residue Gln-64(E7), and of the CD-turn are found to lag significantly (100-300 ns) behind local rearrangements around the heme such as heme tilting, iron motion out of the heme plane, and swinging of the mutated residue Tyr-29(B10), all of which occur promptly (< or =3 ns). Over the same delayed time range, CO is observed to migrate from a cavity distal to the heme known to bind xenon (called Xe4) to another such cavity proximal to the heme (Xe1). We propose that the extended relaxation of the globin moiety reflects reequilibration among conformational substates known to play an essential role in controlling protein function.


    Related Citations: 
    • The role of cavities in protein dynamics: crystal structure of a photolytic intermediate of a mutant myoglobin.
      Brunori, M.,Vallone, B.,Cutruzzol, F.,Travaglini-Allocatelli, C.,Berendzen, J.,Chu, K.,Sweet, R.M.,Schlichting, I.
      (2000) Proc.Natl.Acad.Sci.USA 97: 2058
    • Structural dynamics of ligand diffusion in the protein matrix: A study on a new myoglobin mutant Y(B10) Q(E7) R(E10)
      Brunori, M.,Cutruzzol, F.,Savino, C.,Travaglini-Allocatelli, C.,Vallone, B.,Gibson, Q.H.
      (1999) Biophys.J. 76: 1259


    Organizational Affiliation

    Laboratoire de Cristallographie et de Cristallogénèse des Protéines, UMR 9015, Institut de Biologie Structurale/Commissariat à l'Energie Atomique/Université Joseph Fourier, and European Synchrotron Radiation Facility, Grenoble, France. bourgeoi@lccp.ibs.fr




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Myoglobin
A
154Physeter catodonMutation(s): 4 
Gene Names: MB
Find proteins for P02185 (Physeter catodon)
Go to Gene View: MB
Go to UniProtKB:  P02185
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: 1.6 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.150 
  • Space Group: P 6
Unit Cell:
Length (Å)Angle (°)
a = 91.200α = 90.00
b = 91.200β = 90.00
c = 45.712γ = 120.00
Software Package:
Software NamePurpose
PROWdata reduction
CNSrefinement
CCP4data scaling
PROWdata scaling
SPECdata reduction
SPECdata collection
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-07-29
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2015-09-09
    Type: Version format compliance
  • Version 1.4: 2018-06-27
    Type: Data collection, Database references