3WFT

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.126 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

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

  • DOI: 10.1039/c4cc05448b
  • Primary Citation of Related Structures:  

  • 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 cl ...

    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.


    Organizational Affiliation

    Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita 565-0871, Japan. thayashi@chem.eng.osaka-u.ac.jp.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Myoglobin
A
153Equus caballusMutation(s): 0 
Gene Names: MB
Find proteins for P68082 (Equus caballus)
Go to Gene View: MB
Go to UniProtKB:  P68082
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
J1R
Query on J1R

Download SDF File 
Download CCD File 
A
(1R,19R) cobalt tetradehydrocorrin
C33 H37 Co N4 O4
DBXMOQHUTDEXAY-ZNBLAKOKSA-M
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
J1S
Query on J1S

Download SDF File 
Download CCD File 
A
(1S,19S) cobalt tetradehydrocorrin
C33 H37 Co N4 O4
DBXMOQHUTDEXAY-MLGYITDRSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.126 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 34.975α = 90.00
b = 28.987β = 106.14
c = 63.214γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
SERGUIdata collection
HKL-2000data reduction
HKL-2000data scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-12-03
    Type: Initial release
  • Version 1.1: 2017-11-22
    Type: Refinement description