Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 18297.87 
• Atom Count: 1390 
• Residue Count: 154 
• Unique protein chains: 1

1MYZ

CO COMPLEX OF MYOGLOBIN MB-YQR AT RT SOLVED FROM LAUE DATA.

• DOI: 10.2210/pdb1MYZ/pdb

• Classification: OXYGEN STORAGE/TRANSPORT
• Organism(s): Physeter macrocephalus
• Expression System: Escherichia coli
• Mutation(s): 4 


• Deposited: 2002-10-04 Released: 2003-08-19 
• Deposition Author(s): Bourgeois, D., Vallone, B., Schotte, F., Arcovito, A., Miele, A.E., Sciara, G., Wulff, M., Anfinrud, P., Brunori, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.6 Å
• R-Value Free: 0.184 
• R-Value Work: 0.166 

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

• PubMed: 12847289 
• DOI: 10.1073/pnas.1430900100
• Primary Citation of Related Structures:  
  1MZ0


• 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 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.

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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




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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. [e-mail]

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Myoglobin	A	154	Physeter macrocephalus	Mutation(s): 4  Gene Names: MB
Find proteins for P02185 (Physeter macrocephalus) Go to Gene View: MB Go to UniProtKB:  P02185

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
SO4	A	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
HEM	A	PROTOPORPHYRIN IX CONTAINING FE HEME C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
CMO	A	CARBON MONOXIDE C O UGFAIRIUMAVXCW-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.6 Å
• R-Value Free: 0.184 
• R-Value Work: 0.166 
• Space Group: P 6

Unit Cell:

Length (Å)	Angle (°)
a = 91.200	α = 90.00
b = 91.200	β = 90.00
c = 45.712	γ = 120.00

Software Package:

Software Name	Purpose
PROW	data reduction
PROW	data scaling
SPEC	data collection
CNS	refinement
SPEC	data reduction
CNS	phasing
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-10-04 
• Released Date: 2003-08-19 
• Deposition Author(s): Bourgeois, D., Vallone, B., Schotte, F., Arcovito, A., Miele, A.E., Sciara, G., Wulff, M., Anfinrud, P., Brunori, M.

Revision History 

• Version 1.0: 2003-08-19
  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: 2017-10-11
  Type: Advisory