Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 18173.80 
• Atom Count: 1280 
• Residue Count: 154 
• Unique protein chains: 1

1F63

CRYSTAL STRUCTURE OF DEOXY SPERM WHALE MYOGLOBIN MUTANT Y(B10)Q(E7)R(E10)

• DOI: 10.2210/pdb1F63/pdb

• Classification: OXYGEN STORAGE/TRANSPORT
• Organism(s): Physeter catodon
• Expression System: Escherichia coli
• Mutation(s): 3 


• Deposited: 2000-06-20 Released: 2000-07-19 
• Deposition Author(s): Brunori, M., Cutruzzola, F., Savino, C., Travaglini-Allocatelli, C., Vallone, B., Gibson, Q.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.8 Å
• R-Value Free: 0.220 
• R-Value Work: 0.169 

Literature

Structural dynamics of ligand diffusion in the protein matrix: A study on a new myoglobin mutant Y(B10) Q(E7) R(E10).

Brunori, M., Cutruzzola, F., Savino, C., Travaglini-Allocatelli, C., Vallone, B., Gibson, Q.H.

(1999) Biophys.J. 76: 1259-1269

• PubMed: 10049310 
• DOI: 10.1016/S0006-3495(99)77289-9
• Primary Citation of Related Structures:  
  1F65
• Also Cited By: 1DXD, 1DXC


• PubMed Abstract: 
  

A triple mutant of sperm whale myoglobin (Mb) [Leu(B10) --> Tyr, His(E7) --> Gln, and Thr(E10) --> Arg, called Mb-YQR], investigated by stopped-flow, laser photolysis, crystallography, and molecular dynamics (MD) simulations, proved to be quite unusual. Rebinding of photodissociated NO, O2, and CO from within the protein (in a "geminate" mode) allows us to reach general conclusions about dynamics and cavities in proteins. The 3D structure of oxy Mb-YQR shows that bound O2 makes two H-bonds with Tyr(B10)29 and Gln(E7)64; on deoxygenation, these two residues move toward the space occupied by O2. The bimolecular rate constant for NO binding is the same as for wild-type, but those for CO and O2 binding are reduced 10-fold. While there is no geminate recombination with O2 and CO, geminate rebinding of NO displays an unusually large and very slow component, which is pretty much abolished in the presence of xenon. These results and MD simulations suggest that the ligand migrates in the protein matrix to a major "secondary site," located beneath Tyr(B10)29 and accessible via the motion of Ile(G8)107; this site is different from the "primary site" identified by others who investigated the photolyzed state of wild-type Mb by crystallography. Our hypothesis may rationalize the O2 binding properties of Mb-YQR, and more generally to propose a mechanism of control of ligand binding and dissociation in hemeproteins based on the dynamics of side chains that may (or may not) allow access to and direct temporary sequestration of the dissociated ligand in a docking site within the protein. This interpretation suggests that very fast (picosecond) fluctuations of amino acid side chains may play a crucial role in controlling O2 delivery to tissue at a rate compatible with physiology.

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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.,Cutruzzola, F.,Travaglini-Allocatelli, C.,Berendzen, J.,Chu, K.,Sweet, R.M.,Schlichting, I.
  (2000) Proc.Natl.Acad.Sci.USA 97: 2058
• Does Picosecond Protein Dynamics Have a Survival Value?
  Brunori, M.,Cutruzzola, F.,Savino, C.,Travaglini-Allocatelli, C.,Vallone, B.,Gibson, Q.H.
  (1999) TRENDS BIOCHEM.SCI. 24: 253




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Organizational Affiliation: 

Department of Biochemical Sciences and CNR Center of Molecular Biology, University of Rome "La Sapienza," Rome, Italy. [e-mail]

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
MYOGLOBIN	A	154	Physeter catodon	Mutation(s): 3  Gene Names: MB
Find proteins for P02185 (Physeter catodon) Go to Gene View: MB Go to UniProtKB:  P02185

Small Molecules

Ligands 2 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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.8 Å
• R-Value Free: 0.220 
• R-Value Work: 0.169 
• Space Group: P 6

Unit Cell:

Length (Å)	Angle (°)
a = 91.520	α = 90.00
b = 91.520	β = 90.00
c = 45.980	γ = 120.00

Software Package:

Software Name	Purpose
FFT	model building
SCALEPACK	data scaling
REFMAC	refinement
DENZO	data reduction
FFT	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2000-06-20 
• Released Date: 2000-07-19 
• Deposition Author(s): Brunori, M., Cutruzzola, F., Savino, C., Travaglini-Allocatelli, C., Vallone, B., Gibson, Q.H.

Revision History 

• Version 1.0: 2000-07-19
  Type: Initial release
• Version 1.1: 2008-04-27
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance