Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 17.97 kDa 
• Atom Count: 1560 
• Modelled Residue Count: 154 
• Deposited Residue Count: 154 
• Unique protein chains: 1

3H58

Myoglobin Cavity Mutant H64LV68N Met form

• DOI: 10.2210/pdb3H58/pdb

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


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.219 
• R-Value Work: 0.196 

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

• PubMed: 19655795 
• DOI: 10.1021/ja903409j
• Primary Citation of Related Structures:  
  3H58, 3H57


• 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 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.

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Organizational Affiliation: 

Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, USA. [e-mail]

Macromolecules

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	B [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.219 
• R-Value Work: 0.196 
• Space Group: P 6

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.13	α = 90
b = 90.13	β = 90
c = 45.26	γ = 120

Software Package:

Software Name	Purpose
d*TREK	data processing
CNS	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
CrystalClear	data reduction
d*TREK	data scaling
CNS	phasing

Structure Validation

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
  Changes: Version format compliance