8SSD

Methionine synthase, C-terminal fragment, Cobalamin and Reactivation Domains from Thermus thermophilus HB8

• PDB DOI: https://doi.org/10.2210/pdb8SSD/pdb

• Classification: TRANSFERASE
• Organism(s): Thermus thermophilus HB8
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-05-08 Released: 2023-10-11 
• Deposition Author(s): Yamada, K., Mendoza, J., Koutmos, M.
• Funding Organization(s): National Science Foundation (NSF, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.301 
• R-Value Work: 0.265 

Literature

Structure of full-length cobalamin-dependent methionine synthase and cofactor loading captured in crystallo

Mendoza, J., Purchal, M., Yamada, K., Koutmos, M.

(2023) Nat Commun 14: 6365

• DOI: https://doi.org/10.1038/s41467-023-42037-4

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 3-mer - A3 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 175.82 kDa 
• Atom Count: 12,452 
• Modelled Residue Count: 1,513 
• Deposited Residue Count: 1,569 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methionine synthase	A, B [auth C], C [auth B]	523	Thermus thermophilus HB8	Mutation(s): 0  Gene Names: TTHA0618 EC: 2.1.1.13
UniProt
Find proteins for Q5SKM5 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SKM5  Go to UniProtKB:  Q5SKM5

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.301 
• R-Value Work: 0.265 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.177	α = 90
b = 96.177	β = 90
c = 356.04	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-10-11 
Deposition Author(s): Yamada, K., Mendoza, J., Koutmos, M.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	1945174

Revision History  

• Version 1.0: 2023-10-11
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Database references