4H2L

Deer mouse hemoglobin in hydrated format


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.779 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.162 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Deer mouse hemoglobin exhibits a lowered oxygen affinity owing to mobility of the E helix.

Inoguchi, N.Oshlo, J.R.Natarajan, C.Weber, R.E.Fago, A.Storz, J.F.Moriyama, H.

(2013) Acta Crystallogr.,Sect.F 69: 393-398

  • DOI: 10.1107/S1744309113005708

  • PubMed Abstract: 
  • The deer mouse, Peromyscus maniculatus, exhibits altitude-associated variation in hemoglobin oxygen affinity. To examine the structural basis of this functional variation, the structure of the hemoglobin was solved. Recombinant hemoglobin was express ...

    The deer mouse, Peromyscus maniculatus, exhibits altitude-associated variation in hemoglobin oxygen affinity. To examine the structural basis of this functional variation, the structure of the hemoglobin was solved. Recombinant hemoglobin was expressed in Escherichia coli and was purified by ion-exchange chromatography. Recombinant hemoglobin was crystallized by the hanging-drop vapor-diffusion method using polyethylene glycol as a precipitant. The obtained orthorhombic crystal contained two subunits in the asymmetric unit. The refined structure was interpreted as the aquo-met form. Structural comparisons were performed among hemoglobins from deer mouse, house mouse and human. In contrast to human hemoglobin, deer mouse hemoglobin lacks the hydrogen bond between α1Trp14 in the A helix and α1Thr67 in the E helix owing to the Thr67Ala substitution. In addition, deer mouse hemoglobin has a unique hydrogen bond at the α1β1 interface between residues α1Cys34 and β1Ser128.


    Organizational Affiliation

    School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Alpha-globin
A
141Peromyscus maniculatusMutation(s): 0 
Gene Names: HBA (Hba)
Find proteins for A4ZQ95 (Peromyscus maniculatus)
Go to UniProtKB:  A4ZQ95
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Beta globin
B
146Peromyscus maniculatusMutation(s): 0 
Gene Names: HBB-T1 (HBB, HBB-T2)
Find proteins for C5MQT7 (Peromyscus maniculatus)
Go to UniProtKB:  C5MQT7
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download SDF File 
Download CCD File 
A, B
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: 1.779 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.162 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 76.675α = 90.00
b = 80.061β = 90.00
c = 86.848γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
CrystalCleardata collection
HKL-2000data reduction
PHENIXmodel building
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-04-10
    Type: Initial release
  • Version 1.1: 2013-06-19
    Type: Database references