3H58

Myoglobin Cavity Mutant H64LV68N Met form

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

Literature

Optical detection of disordered water within a protein cavity.

Goldbeck, R.A., Pillsbury, M.L., Jensen, R.A., Mendoza, J.L., Nguyen, R.L., Olson, J.S., Soman, J., Kliger, D.S., Esquerra, R.M.

(2009) J.Am.Chem.Soc. 131: 12265-12272

  • DOI: 10.1021/ja903409j
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Internal water molecules are important to protein structure and function, but positional disorder and low occupancies can obscure their detection by X-ray crystallography. Here, we show that water can be detected within the distal cavities of myoglob ...

    Internal water molecules are important to protein structure and function, but positional disorder and low occupancies can obscure their detection by X-ray crystallography. Here, we show that water can be detected within the distal cavities of myoglobin mutants by subtle changes in the absorbance spectrum of pentacoordinate heme, even when the presence of solvent is not readily observed in the corresponding crystal structures. A well-defined, noncoordinated water molecule hydrogen bonded to the distal histidine (His64) is seen within the distal heme pocket in the crystal structure of wild type (wt) deoxymyoglobin. Displacement of this water decreases the rate of ligand entry into wt Mb, and we have shown previously that the entry of this water is readily detected optically after laser photolysis of MbCO complexes. However, for L29F and V68L Mb no discrete positions for solvent molecules are seen in the electron density maps of the crystal structures even though His64 is still present and slow rates of ligand binding indicative of internal water are observed. In contrast, time-resolved perturbations of the visible absorption bands of L29F and V68L deoxyMb generated after laser photolysis detect the entry and significant occupancy of water within the distal pockets of these variants. Thus, the spectral perturbation of pentacoordinate heme offers a potentially robust system for measuring nonspecific hydration of the active sites of heme proteins.

    Organizational Affiliation: 

    Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, USA. goldbeck@chemistry.ucsc.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Myoglobin
A
154Physeter catodonMutation(s): 3 
Gene Names: MB
Find proteins for P02185 (Physeter catodon)
Go to Gene View: MB
Go to UniProtKB:  P02185
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.196 
  • Space Group: P 6
Unit Cell:
Length (Å)Angle (°)
a = 90.130α = 90.00
b = 90.130β = 90.00
c = 45.260γ = 120.00
Software Package:
Software NamePurpose
CNSphasing
PDB_EXTRACTdata extraction
CNSrefinement
d*TREKdata scaling
CrystalCleardata reduction
d*TREKdata processing
CrystalCleardata collection

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2009-04-21 
  • Released Date: 2009-05-05 
  • Deposition Author(s): Soman, J., Olson, J.S.

Revision History 

  • Version 1.0: 2009-05-05
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance