9CBP | pdb_00009cbp

Methionine synthase from Thermus thermophilus HB8, Homocysteine, Folate, and Cobalamin Domains, Pre-Catalytic State (Pre-Hcy-on)

• PDB DOI: https://doi.org/10.2210/pdb9CBP/pdb

• Classification: TRANSFERASE
• Organism(s): Thermus thermophilus HB8
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2024-06-19 Released: 2025-06-25 
• 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: 2.45 Å
• R-Value Free: 
  0.233 (Depositor), 0.234 (DCC) 
• R-Value Work: 
  0.161 (Depositor), 0.178 (DCC) 
• R-Value Observed: 
  0.165 (Depositor) 

Starting Model: experimental

Literature

Methionine synthase from Thermus thermophilus HB8, Homocysteine, Folate, and Cobalamin Domains, Pre-Catalytic State (Pre-Hcy-on)

Mendoza, J., Yamada, K., Koutmos, M.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 98.58 kDa 
• Atom Count: 7,037 
• Modeled Residue Count: 862 
• Deposited Residue Count: 877 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methionine synthase	A	877	Thermus thermophilus HB8	Mutation(s): 7  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

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
B12 (Subject of Investigation/LOI)	K [auth A]	COBALAMIN C62 H89 Co N13 O14 P LKVIQTCSMMVGFU-DWSMJLPVSA-N
THG (Subject of Investigation/LOI)	M [auth A]	(6S)-5,6,7,8-TETRAHYDROFOLATE C19 H23 N7 O6 MSTNYGQPCMXVAQ-RYUDHWBXSA-N
HCS (Subject of Investigation/LOI)	D [auth A]	2-AMINO-4-MERCAPTO-BUTYRIC ACID C4 H9 N O2 S FFFHZYDWPBMWHY-VKHMYHEASA-N
GOL	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], L [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN (Subject of Investigation/LOI)	B [auth A], N [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
TME (Subject of Investigation/LOI)	O [auth A]	PROPANE C3 H8 ATUOYWHBWRKTHZ-UHFFFAOYSA-N
K	C [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free:  0.233 (Depositor), 0.234 (DCC) 
• R-Value Work:  0.161 (Depositor), 0.178 (DCC) 
• R-Value Observed: 0.165 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.949	α = 90
b = 83.82	β = 90
c = 163.715	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-06-25 
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: 2025-06-25
  Type: Initial release
  
• Version 2.0: 2025-09-03
  Type: Coordinate replacement
  Reason: Model completeness
  Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Non-polymer description, Refinement description, Structure summary
• Version 3.0: 2026-05-13
  Type: Coordinate replacement
  Reason: Model completeness
  Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Non-polymer description, Polymer sequence, Refinement description, Source and taxonomy, Structure summary