Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 30.72 kDa 
• Atom Count: 2245 
• Residue Count: 263 
• Unique protein chains: 1

1S61

Crystal Structure of "Truncated" Hemoglobin N (HbN) from Mycobacterium tuberculosis, Soaked with Butyl-isocyanide

• DOI: 10.2210/pdb1S61/pdb

• Classification: OXYGEN STORAGE/TRANSPORT
• Organism(s): Mycobacterium tuberculosis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-01-22 Released: 2004-06-29 
• Deposition Author(s): Milani, M., Pesce, A., Ouellet, Y., Dewilde, S., Friedman, J., Ascenzi, P., Guertin, M., Bolognesi, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.251 
• R-Value Work: 0.194 
• R-Value Observed: 0.197 

Literature

Heme-ligand tunneling in group I truncated hemoglobins

Milani, M., Pesce, A., Ouellet, Y., Dewilde, S., Friedman, J., Ascenzi, P., Guertin, M., Bolognesi, M.

(2004) J Biol Chem 279: 21520-21525

• PubMed: 15016811 
• DOI: 10.1074/jbc.M401320200
• Primary Citation of Related Structures:  
  1UVY, 1UVX, 1S61, 1S56


• PubMed Abstract: 
  

Truncated hemoglobins (trHbs) are small hemoproteins forming a separate cluster within the hemoglobin superfamily; their functional roles in bacteria, plants, and unicellular eukaryotes are marginally understood. Crystallographic investigations have shown that the trHb fold (a two-on-two alpha-helical sandwich related to the globin fold) hosts a protein matrix tunnel system offering a potential path for ligand diffusion to the heme distal site. The tunnel topology is conserved in group I trHbs, although with modulation of its size/structure. Here, we present a crystallographic investigation on trHbs from Mycobacterium tuberculosis, Chlamydomonas eugametos, and Paramecium caudatum, showing that treatment of trHb crystals under xenon pressure leads to binding of xenon atoms at specific (conserved) sites along the protein matrix tunnel. The crystallographic results are in keeping with data from molecular dynamics simulations, where a dioxygen molecule is left free to diffuse within the protein matrix. Modulation of xenon binding over four main sites is related to the structural properties of the tunnel system in the three trHbs and may be connected to their functional roles. In a parallel crystallographic investigation on M. tuberculosis trHbN, we show that butyl isocyanide also binds within the apolar tunnel, in excellent agreement with concepts derived from the xenon binding experiments. These results, together with recent data on atypical CO rebinding kinetics to group I trHbs, underline the potential role of the tunnel system in supporting diffusion, but also accumulation in multiple copies, of low polarity ligands/molecules within group I trHbs.

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Organizational Affiliation: 

Giannina Gaslini Institute, Largo G. Gaslini, 5. 16147 Genoa, Italy.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemoglobin-like protein HbN	A, B	136	Mycobacterium tuberculosis	Mutation(s): 0  Gene Names: glbN, Rv1542c, MT1594, MTCY48.23, MB1569C
Find proteins for P9WN25 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WN25  Go to UniProtKB:  P9WN25

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	A, B	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
PO4	A, B	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
NBN	A	N-BUTYL ISOCYANIDE C5 H9 N FSBLVBBRXSCOKU-UHFFFAOYSA-N
K	A	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
CYN	A, B	CYANIDE ION C N XFXPMWWXUTWYJX-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.251 
• R-Value Work: 0.194 
• R-Value Observed: 0.197 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.534	α = 90
b = 61.432	β = 90
c = 91.785	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-01-22 
• Released Date: 2004-06-29 
Deposition Author(s): Milani, M., Pesce, A., Ouellet, Y., Dewilde, S., Friedman, J., Ascenzi, P., Guertin, M., Bolognesi, M.

Revision History 

• Version 1.0: 2004-06-29
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2020-01-15
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary