3V2Z | pdb_00003v2z

Nitrite Bound Chlorin Substituted Myoglobin- Method 2

• PDB DOI: https://doi.org/10.2210/pdb3V2Z/pdb

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


• Deposited: 2011-12-12 Released: 2012-11-21 
• Deposition Author(s): Yi, J., Thomas, L.M., Ricther-Addo, G.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.232 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.181 (DCC) 
• R-Value Observed: 
  0.186 (Depositor) 

Starting Model: experimental

Literature

Distal pocket control of nitrite binding in myoglobin

Yi, J., Thomas, L.M., Richter-Addo, G.B.

(2012) Angew Chem Int Ed Engl 51: 3625-3627

• PubMed: 22383424 
• DOI: https://doi.org/10.1002/anie.201200010
• Primary Citation Related Structures: 
  3V2V, 3V2Z

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Organizational Affiliation: 
• Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK 73019, 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: 17.87 kDa 
• Atom Count: 1,394 
• 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
HKL	B [auth A]	Fe(III) pyropheophorbide-a methyl ester C34 H34 Fe N4 O3 IHBXBEKUKOKKKZ-COBSGTNCSA-M
SO4	E [auth A], F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
NO2	C [auth A], D [auth A]	NITRITE ION N O2 IOVCWXUNBOPUCH-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.232 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.181 (DCC) 
• R-Value Observed: 0.186 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.285	α = 90
b = 30.36	β = 104.94
c = 64.06	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: 2012-11-21 
Deposition Author(s): Yi, J., Thomas, L.M., Ricther-Addo, G.B.

Revision History  

• Version 1.0: 2012-11-21
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description