3DHR | pdb_00003dhr

Crystal Structure Determination of Methemoglobin from Pigeon at 2 Angstrom Resolution (Columba livia)

• PDB DOI: https://doi.org/10.2210/pdb3DHR/pdb

• Classification: OXYGEN STORAGE, OXYGEN TRANSPORT
• Organism(s): Columba livia
• Mutation(s): No 


• Deposited: 2008-06-18 Released: 2009-06-30 
• Deposition Author(s): Sathya Moorthy, P., Neelagandan, K., Balasubramanian, M., Ponnuswamy, M.N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.276 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.243 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.247 (Depositor) 

Starting Model: experimental

Literature

Purification, Crystallization and X-ray Diffraction Studies of Pigeon Hemoglobin

Sathya Moorthy, P., Neelagandan, K., Balasubramanian, M., Ponnuswamy, M.N.

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.

Biological Assembly 2  

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 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 4 generated by PISA (software)

Biological Assembly 5  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 5 generated by PISA (software)

Biological Assembly 6  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 6 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 130.82 kDa 
• Atom Count: 9,387 
• Modeled Residue Count: 1,144 
• Deposited Residue Count: 1,152 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemoglobin subunit alpha-A	A, C, E, G	142	Columba livia	Mutation(s): 0
UniProt
Find proteins for P21871 (Columba livia) Explore P21871  Go to UniProtKB:  P21871

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemoglobin subunit beta	B, D, F, H	146	Columba livia	Mutation(s): 0
UniProt
Find proteins for P11342 (Columba livia) Explore P11342  Go to UniProtKB:  P11342

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	I [auth A], J [auth B], K [auth C], L [auth D], M [auth E], N [auth F], O [auth G], P [auth H]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.276 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.243 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.247 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.659	α = 78.78
b = 65.322	β = 89.9
c = 103.733	γ = 65.3

Software Package:

Software Name	Purpose
REFMAC	refinement
MAR345	data collection
AUTOMAR	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-06-30 
Deposition Author(s): Sathya Moorthy, P., Neelagandan, K., Balasubramanian, M., Ponnuswamy, M.N.

Revision History  

• Version 1.0: 2009-06-30
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2016-12-21
  Changes: Other
• Version 1.3: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description