3VAU | pdb_00003vau

Myoglobin nitrite structure: nitriheme modified

• PDB DOI: https://doi.org/10.2210/pdb3VAU/pdb

• Classification: OXYGEN TRANSPORT
• Organism(s): Equus caballus
• Mutation(s): No 


• Deposited: 2011-12-29 Released: 2012-04-11 
• Deposition Author(s): Yi, J., Richter-Addo, G.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.237 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.173 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.176 (Depositor) 

Starting Model: experimental

Literature

Unveiling the three-dimensional structure of the green pigment of nitrite-cured meat

Yi, J., Richter-Addo, G.B.

(2012) Chem Commun (Camb) 48: 4172-4174

• PubMed: 22430128 
• DOI: https://doi.org/10.1039/c2cc31065a
• Primary Citation of Related Structures:  
  3VAU


• PubMed Abstract: 
  

  The 1.70 Å-resolution X-ray crystal structure of the green pigment occasionally present in nitrite-cured meat reveals a regiospecific nitration of the heme at the 2-vinyl position; the regiospecificity is favored on steric grounds, and results in movement of the 2-nitrovinyl moiety into the plane of the 24-atom heme macrocycle.

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Organizational Affiliation: 

Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma, USA. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 17.79 kDa 
• Atom Count: 1,336 
• Modelled Residue Count: 151 
• Deposited Residue Count: 153 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Myoglobin	A	153	Equus caballus	Mutation(s): 0  EC: 1.11.1 (UniProt), 1.7 (UniProt)
UniProt
Find proteins for P68082 (Equus caballus) Explore P68082  Go to UniProtKB:  P68082

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NTE	B [auth A]	[3,3'-{7-ethenyl-3,8,13,17-tetramethyl-12-[(E)-2-nitroethenyl]porphyrin-2,18-diyl-kappa~4~N~21~,N~22~,N~23~,N~24~}dipro panoato(2-)]iron C34 H31 Fe N5 O6 MBEUICWDKPMPCN-RXJYIKGQSA-L
SO4	D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
NO2	C [auth A]	NITRITE ION N O2 IOVCWXUNBOPUCH-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.237 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.173 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.176 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.14	α = 90
b = 28.423	β = 105.5
c = 62.867	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
PHASER	phasing
REFMAC	refinement
d*TREK	data reduction
d*TREK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-04-11 
Deposition Author(s): Yi, J., Richter-Addo, G.B.

Revision History  

• Version 1.0: 2012-04-11
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary