1V75

Crystal structure of hemoglobin D from the Aldabra giant tortoise (Geochelone gigantea) at 2.0 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystallization and preliminary X-ray diffraction study of hemoglobin D from the Aldabra giant tortoise, Geochelone gigantea.

Kuwada, T.Hasegawa, T.Satoh, I.Ishikawa, K.Shishikura, F.

(2003) Protein Pept.Lett. 10: 422-425


  • PubMed Abstract: 
  • Hemoglobin D (Hb D) from the Aldabra giant tortoise, Geochelone gigantea, was crystallized by the hanging drop vapor diffusion technique with a precipitant solution containing 10% polyethylene glycol 3350 and 50 mM HEPES-Na, pH 7.5. The Hb D crystals ...

    Hemoglobin D (Hb D) from the Aldabra giant tortoise, Geochelone gigantea, was crystallized by the hanging drop vapor diffusion technique with a precipitant solution containing 10% polyethylene glycol 3350 and 50 mM HEPES-Na, pH 7.5. The Hb D crystals of G. gigantea, which diffract to at least a 2.0 A resolution, belong to the monoclinic space group C2 with unit cell dimensions of a = 112.1 A, b = 62.4 A, c = 54.0 A, and beta = 110.3 degrees. One alphabeta dimer molecule of Hb D existed in an asymmetric unit, with a calculated value of Vm of 2.77 A(3)Da(-1).


    Organizational Affiliation

    Institute of Quantum Science, Nihon University, Funabashi 274-8501, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hemoglobin D alpha chain
A
141Aldabrachelys giganteaMutation(s): 0 
Find proteins for P83134 (Aldabrachelys gigantea)
Go to UniProtKB:  P83134
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Hemoglobin A and D beta chain
B
146Aldabrachelys giganteaMutation(s): 0 
Find proteins for P83133 (Aldabrachelys gigantea)
Go to UniProtKB:  P83133
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: 2.02 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.188 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 112.142α = 90.00
b = 62.374β = 110.26
c = 53.980γ = 90.00
Software Package:
Software NamePurpose
CNXphasing
CNXrefinement
CrystalCleardata scaling
CrystalCleardata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-12-30
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance