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: 1.60 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.150 
  • R-Value Observed: 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 U S A 100: 8704-8709

  • DOI: 10.1073/pnas.1430900100
  • Primary Citation of Related Structures:  
    1MZ0, 1MYZ

  • 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: 
    • 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
    • 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 U S A 97: 2058

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
MyoglobinA154Physeter catodonMutation(s): 4 
Gene Names: MB
Find proteins for P02185 (Physeter macrocephalus)
Explore P02185 
Go to UniProtKB:  P02185
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download CCD File 
A
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
SO4
Query on SO4

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

Download CCD File 
A
CARBON MONOXIDE
C O
UGFAIRIUMAVXCW-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.150 
  • Space Group: P 6
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.2α = 90
b = 91.2β = 90
c = 45.712γ = 120
Software Package:
Software NamePurpose
SPECdata collection
PROWdata reduction
CNSrefinement
SPECdata reduction
PROWdata scaling
CCP4data scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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