1T1N

CRYSTAL STRUCTURE OF CARBONMONOXY HEMOGLOBIN

• PDB DOI: https://doi.org/10.2210/pdb1T1N/pdb

• Classification: OXYGEN TRANSPORT
• Organism(s): Trematomus newnesi
• Mutation(s): No 


• Deposited: 1999-03-05 Released: 1999-04-29 
• Deposition Author(s): Mazzarella, L., Vitagliano, L., Savino, C., Zagari, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Work: 0.192 

Literature

Crystal structure of Trematomus newnesi haemoglobin re-opens the root effect question.

Mazzarella, L., D'Avino, R., di Prisco, G., Savino, C., Vitagliano, L., Moody, P.C.E., Zagari, A.

(1999) J Mol Biol 287: 897-906

• PubMed: 10222199 
• DOI: https://doi.org/10.1006/jmbi.1999.2632
• Primary Citation of Related Structures:  
  1T1N


• PubMed Abstract: 
  

  As new structural data have become available, somewhat contrasting explanations of the Root effect in fish haemoglobins (Hb) have been provided. Hb 1 of the Antarctic fish Trematomus newnesi has a nearly pH-independent oxygen affinity, in spite of 95 % sequence identity with Hb 1 of Trematomus (previously named Pagothenia) bernacchii that has a strong Root effect. Here, the 2.2 A R-state structure of Trematomus newnesi Hb 1 is presented. The structure is similar to that of Root effect fish Hbs from Spot and T. bernacchii, suggesting that the differences in the pH dependence cannot be related to the modulation of the R-state. In comparison to T. bernacchii Hb 1, the role of the three mutations Thr41 (C6)alpha-->Ile, Ala97 (G3)alpha-->Ser and His41 (C7)beta-->Tyr at the alpha1beta2-interface is discussed.

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Organizational Affiliation: 

Centro di Studio di Biocristallografia, CNR, Napoli, Italy. [e-mail]

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: 33.24 kDa 
• Atom Count: 2,388 
• Modelled Residue Count: 289 
• Deposited Residue Count: 289 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (HEMOGLOBIN)	A	143	Trematomus newnesi	Mutation(s): 0
UniProt
Find proteins for P45718 (Trematomus newnesi) Explore P45718  Go to UniProtKB:  P45718

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (HEMOGLOBIN)	B	146	Trematomus newnesi	Mutation(s): 0
UniProt
Find proteins for P45720 (Trematomus newnesi) Explore P45720  Go to UniProtKB:  P45720

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: 2.20 Å
• R-Value Work: 0.192 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.17	α = 90
b = 88.06	β = 97.65
c = 55.25	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
MOSFLM	data reduction
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-04-29 
Deposition Author(s): Mazzarella, L., Vitagliano, L., Savino, C., Zagari, A.

Revision History  

• Version 1.0: 1999-04-29
  Type: Initial release
  
• Version 1.1: 2007-10-16
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-12-11
  Changes: Derived calculations
• Version 1.4: 2023-08-23
  Changes: Data collection, Database references, Derived calculations, Refinement description