1V75

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

• PDB DOI: https://doi.org/10.2210/pdb1V75/pdb

• Classification: OXYGEN STORAGE/TRANSPORT
• Organism(s): Aldabrachelys gigantea
• Mutation(s): No 


• Deposited: 2003-12-12 Released: 2003-12-30 
• Deposition Author(s): Kuwada, T., Hasegawa, T., Satoh, I., Ishikawa, K., Shishikura, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.02 Å
• R-Value Free: 
  0.233 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.190 (DCC) 

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: 14529497 
• DOI: https://doi.org/10.2174/0929866033478799
• Primary Citation of Related Structures:  
  1V75


• 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 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).

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Dihedral - D2  (Explore in 3D)
Pseudo Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 33.62 kDa 
• Atom Count: 2,710 
• Modelled Residue Count: 283 
• Deposited Residue Count: 287 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemoglobin D alpha chain	A	141	Aldabrachelys gigantea	Mutation(s): 0
UniProt
Find proteins for P83134 (Aldabrachelys gigantea) Explore P83134  Go to UniProtKB:  P83134

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemoglobin A and D beta chain	B	146	Aldabrachelys gigantea	Mutation(s): 0
UniProt
Find proteins for P83133 (Aldabrachelys gigantea) Explore P83133  Go to UniProtKB:  P83133

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.02 Å
• R-Value Free:  0.233 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.190 (DCC) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.142	α = 90
b = 62.374	β = 110.26
c = 53.98	γ = 90

Software Package:

Software Name	Purpose
CNX	refinement
CrystalClear	data reduction
CrystalClear	data scaling
CNX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-12-30 
Deposition Author(s): Kuwada, T., Hasegawa, T., Satoh, I., Ishikawa, K., Shishikura, F.

Revision History  

• Version 1.0: 2003-12-30
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-10-09
  Changes: Data collection, Database references
• Version 1.4: 2023-12-27
  Changes: Data collection, Database references, Derived calculations