1MLU

NITRIC OXIDE RECOMBINATION TO DOUBLE MUTANTS OF MYOGLOBIN: THE ROLE OF LIGAND DIFFUSION IN A FLUCTUATING HEME POCKET


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Work: 0.143 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Nitric oxide recombination to double mutants of myoglobin: role of ligand diffusion in a fluctuating heme pocket.

Carlson, M.L.Regan, R.Elber, R.Li, H.Phillips Jr., G.N.Olson, J.S.Gibson, Q.H.

(1994) Biochemistry 33: 10597-10606


  • PubMed Abstract: 
  • Picosecond recombination of nitric oxide to the double mutants of myoglobin, His64Gly-Val68Ala and His64Gly.Val68Ile, at E7 and E11, has been studied experimentally and by computation. It is shown that distal residues have a profound effect on NO rec ...

    Picosecond recombination of nitric oxide to the double mutants of myoglobin, His64Gly-Val68Ala and His64Gly.Val68Ile, at E7 and E11, has been studied experimentally and by computation. It is shown that distal residues have a profound effect on NO recombination. Recombination in the mutants may be explained in terms of fluctuating free volume and structure of the heme pocket. The double mutants provide insight into the effects of free volume and steric hindrance on rates of ligand rebinding following photolysis. Water molecules of the first solvation shell replace surface residues deleted by mutation and can block apparent holes in the protein structure. Thus, water molecules extend the time required for ligands to escape significantly to a nanosecond time scale, which is much longer than would be expected for an open heme pocket. Both nearly exponential (G64A68) and markedly nonexponential (native and G64I68) kinetics are observed, a result at variance with expectation from the model of Petrich et al. [Petrich, J.W., Lambry, J.C., Kuczera, K., Karplus, M., Poyart, C., & Martin, J.L. (1991) Biochemistry 30, 3975-3987], which attributes nonexponential kinetics to proximal effects.


    Related Citations: 
    • Crystal Structure of Myoglobin from a Synthetic Gene
      Phillips Jr., G.N.,Arduini, R.M.,Springer, B.A.,Sligar, S.G.
      (1990) Proteins 7: 358
    • High-Resolution Crystal Structures of Distal Histidine Mutants of Sperm Whale Myoglobin
      Quillin, M.L.,Arduini, R.M.,Olson, J.S.,Phillips Jr., G.N.
      (1993) J.Mol.Biol. 234: 140
    • High-Level Expression of Sperm Whale Myoglobin in Escherichia Coli
      Springer, B.A.,Sligar, S.G.
      (1987) Proc.Natl.Acad.Sci.USA 84: 8961
    • Structural and Functional Effects of Apolar Mutations of Val68(E11) in Myoglobin
      Quillin, M.L.,Li, T.,Olson, J.S.,Phillips Jr., G.N.,Dou, Y.,Ikeda-Saito, M.,Regan, R.,Carlson, M.,Gibson, Q.H.,Li, H.,Elber, R.
      () TO BE PUBLISHED --: --


    Organizational Affiliation

    Department of Biochemistry, Molecular and Cell Biology, Cornell University Ithaca, New York 14853.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MYOGLOBIN
A
154Physeter catodonGene 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: 1.9 Å
  • R-Value Work: 0.143 
  • Space Group: P 6
Unit Cell:
Length (Å)Angle (°)
a = 91.200α = 90.00
b = 91.200β = 90.00
c = 45.870γ = 120.00
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1994-08-31
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance