3WFT

Crystal structure of horse heart myoglobin reconstituted with cobalt(II) tetradehydrocorrin

• PDB DOI: https://doi.org/10.2210/pdb3WFT/pdb

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


• Deposited: 2013-07-23 Released: 2014-12-03 
• Deposition Author(s): Mizohata, E., Morita, Y., Oohora, K., Hirata, K., Ohbayashi, J., Inoue, T., Hisaeda, Y., Hayashi, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 0.183 
• R-Value Work: 0.126 
• R-Value Observed: 0.129 

Literature

Co(II)/Co(I) reduction-induced axial histidine-flipping in myoglobin reconstituted with a cobalt tetradehydrocorrin as a methionine synthase model.

Hayashi, T., Morita, Y., Mizohata, E., Oohora, K., Ohbayashi, J., Inoue, T., Hisaeda, Y.

(2014) Chem Commun (Camb) 50: 12560-12563

• PubMed: 25197974 
• DOI: https://doi.org/10.1039/c4cc05448b
• Primary Citation of Related Structures:  
  3WFT, 3WFU


• PubMed Abstract: 
  

  A conjugate between apomyoglobin and cobalt tetradehydrocorrin was prepared to replicate the coordination behavior of cob(I)alamin in methionine synthase. X-ray crystallography reveals that the tetra-coordinated Co(I) species is formed through the cleavage of the axial Co-His93 ligation after the reduction of the penta-coordinated Co(II) cofactor in the heme pocket.

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Organizational Affiliation: 

Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita 565-0871, Japan. [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: 18.68 kDa 
• Atom Count: 1,490 
• Modelled Residue Count: 153 
• 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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
J1S	C [auth A]	(1S,19S) cobalt tetradehydrocorrin C33 H37 Co N4 O4 DBXMOQHUTDEXAY-MLGYITDRSA-M
J1R	B [auth A]	(1R,19R) cobalt tetradehydrocorrin C33 H37 Co N4 O4 DBXMOQHUTDEXAY-ZNBLAKOKSA-M
SO4	D [auth A], E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	F [auth A], G [auth A], H [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 0.183 
• R-Value Work: 0.126 
• R-Value Observed: 0.129 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.975	α = 90
b = 28.987	β = 106.14
c = 63.214	γ = 90

Software Package:

Software Name	Purpose
SERGUI	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-12-03 
Deposition Author(s): Mizohata, E., Morita, Y., Oohora, K., Hirata, K., Ohbayashi, J., Inoue, T., Hisaeda, Y., Hayashi, T.

Revision History  

• Version 1.0: 2014-12-03
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Refinement description
• Version 1.2: 2024-03-20
  Changes: Data collection, Database references, Derived calculations