2Z6N | pdb_00002z6n

Crystal Structure of Carbonmonoxy Hemoglobin D from the Aldabra Giant Tortoise, Geochelone gigantea

• PDB DOI: https://doi.org/10.2210/pdb2Z6N/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Aldabrachelys gigantea
• Mutation(s): No 


• Deposited: 2007-08-04 Released: 2007-08-28 
• Deposition Author(s): Kuwada, T., Hasegawa, T., Sato, I., Ishikawa, K., Shishikura, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free: 
  0.217 (Depositor), 0.213 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.183 (DCC) 

Starting Model: experimental

Literature

Crystal Structure of the Ligated Hemoglobin D from the Aldabra Giant Tortoise, Geochelone gigantea

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

To be published.

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 and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 33.67 kDa 
• Atom Count: 2,767 
• Modeled Residue Count: 287 
• Deposited Residue Count: 287 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemoglobin D subunit alpha	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/D subunit beta	B	146	Aldabrachelys gigantea	Mutation(s): 0
UniProt
Find proteins for P83133 (Aldabrachelys gigantea) Explore P83133  Go to UniProtKB:  P83133

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	C [auth A], E [auth B]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
CMO	D [auth A], F [auth B]	CARBON MONOXIDE C O UGFAIRIUMAVXCW-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free:  0.217 (Depositor), 0.213 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.183 (DCC) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.355	α = 90
b = 62.104	β = 110.22
c = 53.987	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-08-28 
Deposition Author(s): Kuwada, T., Hasegawa, T., Sato, I., Ishikawa, K., Shishikura, F.

Revision History  

• Version 1.0: 2007-08-28
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2018-06-20
  Changes: Data collection, Database references
• Version 1.3: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description