2G12

Photolyzed CO L29F Myoglobin: 316ns


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.062 
  • R-Value Work: 0.053 
  • R-Value Observed: 0.053 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Time-dependent atomic coordinates for the dissociation of carbon monoxide from myoglobin.

Aranda, R.Levin, E.J.Schotte, F.Anfinrud, P.A.Phillips Jr., G.N.

(2006) Acta Crystallogr D Biol Crystallogr 62: 776-783

  • DOI: 10.1107/S0907444906017318
  • Primary Citation of Related Structures:  
    2G0R, 2G12, 2G11, 2G10, 2G0Z, 2G0X, 2G0V, 2G0S, 2G14

  • PubMed Abstract: 
  • Picosecond time-resolved crystallography was used to follow the dissociation of carbon monoxide from the heme pocket of a mutant sperm whale myoglobin and the resultant conformational changes. Electron-density maps have previously been created at var ...

    Picosecond time-resolved crystallography was used to follow the dissociation of carbon monoxide from the heme pocket of a mutant sperm whale myoglobin and the resultant conformational changes. Electron-density maps have previously been created at various time points and used to describe amino-acid side-chain and carbon monoxide movements. In this work, difference refinement was employed to generate atomic coordinates at each time point in order to create a more explicit quantitative representation of the photo-dissociation process. After photolysis the carbon monoxide moves to a docking site, causing rearrangements in the heme-pocket residues, the coordinate changes of which can be plotted as a function of time. These include rotations of the heme-pocket phenylalanine concomitant with movement of the distal histidine toward the solvent, potentially allowing carbon monoxide movement in and out of the protein and proximal displacement of the heme iron. The degree of relaxation toward the intermediate and deoxy states was probed by analysis of the coordinate movements in the time-resolved models, revealing a non-linear progression toward the unbound state with coordinate movements that begin in the heme-pocket area and then propagate throughout the rest of the protein.


    Organizational Affiliation

    Department of Biomolecular Chemistry, University of Wisconsin, Madison, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
MyoglobinA154Physeter catodonMutation(s): 2 
Gene Names: MB
Find proteins for P02185 (Physeter macrocephalus)
Explore P02185 
Go to UniProtKB:  P02185
Protein Feature View
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  • 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: 1.90 Å
  • R-Value Free: 0.062 
  • R-Value Work: 0.053 
  • R-Value Observed: 0.053 
  • 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
CNSrefinement
LAUEGENdata scaling
PROWdata scaling
LSCALEdata scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-07-04
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2013-01-30
    Changes: Database references, Structure summary
  • Version 1.4: 2017-10-18
    Changes: Refinement description