4ODC

Crystal structure of Trematomus bernacchii hemoglobin in a partially cyanided state

• PDB DOI: https://doi.org/10.2210/pdb4ODC/pdb

• Classification: OXYGEN TRANSPORT/PROTEIN BINDING
• Organism(s): Trematomus bernacchii
• Mutation(s): Yes 


• Deposited: 2014-01-10 Released: 2014-12-24 
• Deposition Author(s): Mazzarella, L., Merlino, A., Vitagliano, L., Vergara, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.54 Å
• R-Value Free: 0.197 
• R-Value Work: 0.165 
• R-Value Observed: 0.165 

Literature

Structural modifications induced by the switch from an endogenous bis-histidyl to an exogenous cyanomet hexa-coordination in a tetrameric haemoglobin

Mazzarella, L., Merlino, A., Vitagliano, L., Verde, C., di Prisco, G., Peisach, J., Vergara, A.

(2014) RSC Adv 4: 25852-25856

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: 33.21 kDa 
• Atom Count: 2,821 
• Modelled Residue Count: 289 
• Deposited Residue Count: 289 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemoglobin subunit alpha	A	143	Trematomus bernacchii	Mutation(s): 1
UniProt
Find proteins for P80043 (Trematomus bernacchii) Explore P80043  Go to UniProtKB:  P80043

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemoglobin subunit beta	B	146	Trematomus bernacchii	Mutation(s): 0
UniProt
Find proteins for P80044 (Trematomus bernacchii) Explore P80044  Go to UniProtKB:  P80044

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	D [auth A], F [auth B]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
GOL	G [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CYN	C [auth A], E [auth B]	CYANIDE ION C N XFXPMWWXUTWYJX-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.54 Å
• R-Value Free: 0.197 
• R-Value Work: 0.165 
• R-Value Observed: 0.165 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.88	α = 90
b = 87.88	β = 99.66
c = 55.25	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
SHELXS	phasing
SHELXL-97	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-12-24 
Deposition Author(s): Mazzarella, L., Merlino, A., Vitagliano, L., Vergara, A.

Revision History  

• Version 1.0: 2014-12-24
  Type: Initial release
  
• Version 1.1: 2019-12-11
  Changes: Advisory, Database references, Derived calculations
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description