3LR9 | pdb_00003lr9

X-ray photogenerated ferrous horse heart myoglobin, nitrite adduct

• PDB DOI: https://doi.org/10.2210/pdb3LR9/pdb

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


• Deposited: 2010-02-10 Released: 2010-07-07 
• Deposition Author(s): Yi, J., Orville, A.M., Richter-Addo, G.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 
  0.212 (Depositor), 0.201 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.168 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

Starting Model: experimental

Literature

Synchrotron X-ray-Induced Photoreduction of Ferric Myoglobin Nitrite Crystals Gives the Ferrous Derivative with Retention of the O-Bonded Nitrite Ligand.

Yi, J., Orville, A.M., Skinner, J.M., Skinner, M.J., Richter-Addo, G.B.

(2010) Biochemistry 49: 5969-5971

• PubMed: 20568729 
• DOI: https://doi.org/10.1021/bi100801g
• Primary Citation Related Structures: 
  3LR7, 3LR9


• PubMed Abstract: 
  

  Exposure of a single crystal of the nitrite adduct of ferric myoglobin (Mb) at 100 K to high-intensity synchrotron X-ray radiation resulted in changes in the UV-vis spectrum that can be attributed to reduction of the ferric compound to the ferrous derivative. We employed correlated single-crystal spectroscopy with crystallography to further characterize this photoproduct. The 1.55 A resolution crystal structure of the photoproduct reveals retention of the O-binding mode for binding of nitrite to the iron center. The data are consistent with cryogenic generation and trapping, at 100 K, of a ferrous d(6) Mb(II)(ONO)* complex by photoreduction of the ferric precursor crystals using high-intensity X-ray radiation.

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Organizational Affiliation: 
• Department of Chemistry and Biochemistry, University of Oklahoma, 620 Parrington Oval, Norman, Oklahoma 73019, USA.

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: 17.98 kDa 
• Atom Count: 1,389 
• Modeled Residue Count: 152 
• 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
HEM	B [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
SO4	G [auth A], H [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
NO2	C [auth A], D [auth A], E [auth A], F [auth A]	NITRITE ION N O2 IOVCWXUNBOPUCH-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free:  0.212 (Depositor), 0.201 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.168 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.327	α = 90
b = 28.691	β = 105.64
c = 62.911	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
PHASER	phasing
PHENIX	refinement
d*TREK	data reduction
d*TREK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-07-07 
Deposition Author(s): Yi, J., Orville, A.M., Richter-Addo, G.B.

Revision History  

• Version 1.0: 2010-07-07
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description