9CBR | pdb_00009cbr

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

• PDB DOI: https://doi.org/10.2210/pdb9CBR/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., Menjdoza, J., Koutmos, M.
• Funding Organization(s): National Science Foundation (NSF, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.38 Å
• R-Value Free: 
  0.217 (Depositor), 0.252 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.225 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: experimental

Literature

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

Menjdoza, 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)

Macromolecule Content 

• Total Structure Weight: 97.72 kDa 
• Atom Count: 7,024 
• Modeled Residue Count: 867 
• 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): 10  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 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
B12 (Subject of Investigation/LOI)	D [auth A]	COBALAMIN C62 H89 Co N13 O14 P LKVIQTCSMMVGFU-DWSMJLPVSA-N
C2F (Subject of Investigation/LOI)	B [auth A]	5-METHYL-5,6,7,8-TETRAHYDROFOLIC ACID C20 H25 N7 O6 ZNOVTXRBGFNYRX-STQMWFEESA-N
ZN (Subject of Investigation/LOI)	C [auth A], E [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
NEH (Subject of Investigation/LOI)	G [auth A]	ETHANAMINE C2 H7 N QUSNBJAOOMFDIB-UHFFFAOYSA-N
K	F [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.38 Å
• R-Value Free:  0.217 (Depositor), 0.252 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.225 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.811	α = 90
b = 115.101	β = 90
c = 120.795	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-06-25 
Deposition Author(s): Yamada, K., Menjdoza, 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, Polymer sequence, Refinement description, Source and taxonomy, Structure summary