1HSY | pdb_00001hsy

ORIGIN OF THE PH-DEPENDENT SPECTROSCOPIC PROPERTIES OF PENTACOORDINATE METMYOGLOBIN VARIANTS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Observed: 
    0.163 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1HSY

This is version 1.3 of the entry. See complete history

Literature

Origin of the pH-dependent spectroscopic properties of pentacoordinate metmyoglobin variants.

Bogumil, R.Maurus, R.Hildebrand, D.P.Brayer, G.D.Mauk, A.G.

(1995) Biochemistry 34: 10483-10490

  • DOI: https://doi.org/10.1021/bi00033a021
  • Primary Citation Related Structures: 
    1HSY

  • PubMed Abstract: 

    The pH dependence of the electronic and EPR spectra of two variants of horse heart myoglobin (Mb) in which the distal His64 ligand has been replaced by either Thr or Ile has been studied. Both of these variants exhibit spectroscopic changes with pH that are indicative of a transition between two ferric high-spin forms that occurs with a pKa of 9.49 for the His64Thr variant and 9.26 for the His64Ile variant and that is distinctly different from the pH-dependent spectroscopic changes related to titration of the distal aquo ligand of wild-type Mb. The electronic and EPR spectra of both variants at all values of pH studied are consistent with the presence of a pentacoordinate heme iron center. For the His64Thr variant, a high-resolution (1.9 A) structure determination establishes the lack of the distal aquo ligand and demonstrates an out-of-plane movement of the ferric iron toward the proximal histidine together with a decrease of the Fe-His bond length. Investigation of this pH-linked equilibrium by EPR spectroscopy reveals rhombically split high-spin signals at both pH 7 and 11 with a greater degree of rhombicity exhibited by the alkaline species. We propose that the pH-linked spectroscopic transition exhibited by these distal histidine variants results from the deprotonation of the proximal His93 residue to produce imidazolate ligation at alkaline pH.


  • Organizational Affiliation
    • Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, Canada.

Macromolecule Content 

  • Total Structure Weight: 17.66 kDa 
  • Atom Count: 1,297 
  • Modeled Residue Count: 153 
  • Deposited Residue Count: 153 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
MYOGLOBIN153Equus caballusMutation(s): 0 
Gene Names: SYNTHETIC GENE
EC: 1.11.1 (UniProt), 1.7 (UniProt)
UniProt
Find proteins for P68082 (Equus caballus)
Explore P68082 
Go to UniProtKB:  P68082
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP68082
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM

Query on HEM



Download:Ideal Coordinates CCD File
C [auth A]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
SO4

Query on SO4



Download:Ideal Coordinates CCD File
B [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Observed: 0.163 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.403α = 90
b = 28.856β = 107.2
c = 35.79γ = 90
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1995-02-27
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-02-07
    Changes: Data collection, Database references, Derived calculations, Other