5LFG

X-ray structure of a new fully ligated carbomonoxy form of Trematomus newnesi hemoglobin (Hb1TnCO).


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Fine Sampling of the RT Quaternary-Structure Transition of a Tetrameric Hemoglobin.

Vitagliano, L.Mazzarella, L.Merlino, A.Vergara, A.

(2017) Chemistry 23: 605-613

  • DOI: 10.1002/chem.201603421

  • PubMed Abstract: 
  • Although the end points of the functional transitions of tetrameric hemoglobins (Hbs) have been well characterized, atomic-resolution data on R-T intermediate states are extremely limited. Herein, the X-ray structures of two independent tetramers of ...

    Although the end points of the functional transitions of tetrameric hemoglobins (Hbs) have been well characterized, atomic-resolution data on R-T intermediate states are extremely limited. Herein, the X-ray structures of two independent tetramers of the fully ligated carbomonoxy form of Trematomus newnesi hemoglobin (Hb1Tn) within the same crystal are described. These structures show peculiar features in the heme pocket, EF corner, and tertiary/quaternary structure. Distal histidine side chains have a propensity to swing out of the heme pocket and thus allow compression of the EF corner. In this rotameric state, the distal His group does not interact with the CO ligand, consistent with FTIR spectra recorded in solution. At the quaternary-structure level, one tetramer is an intermediate R-T state, whereas the other assumes a T-like structure. Altogether, the structures of these tetramers provide the best available atomic-level picture of the R→T transition of vertebrate Hbs.


    Organizational Affiliation

    Institute of Biostructures and Biomaging, CNR, Via Mezzocannone 16, 80134, Napoli, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hemoglobin subunit alpha-1
A, C
143Trematomus newnesiMutation(s): 0 
Gene Names: hba1
Find proteins for P45718 (Trematomus newnesi)
Go to UniProtKB:  P45718
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Hemoglobin subunit beta-1/2
B, D
146Trematomus newnesiMutation(s): 0 
Find proteins for P45720 (Trematomus newnesi)
Go to UniProtKB:  P45720
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download SDF File 
Download CCD File 
A, B, C, D
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
CMO
Query on CMO

Download SDF File 
Download CCD File 
A, B, C, D
CARBON MONOXIDE
C O
UGFAIRIUMAVXCW-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
ACE
Query on ACE
A, C
NON-POLYMERC2 H4 O

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.181 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 86.206α = 90.00
b = 87.256β = 101.81
c = 109.648γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
SHELXLrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-08-09
    Type: Initial release