7L9U | pdb_00007l9u

Crystal Structure of S-adenosylmethionine-dependent methyltransferase UmaA from Mycobacterium tuberculosis in complex with a 12-mer PEG

• PDB DOI: https://doi.org/10.2210/pdb7L9U/pdb

• Classification: TRANSFERASE
• Organism(s): Mycobacterium tuberculosis H37Rv
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-01-05 Released: 2021-02-10 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 
  0.175 (Depositor), 0.176 (DCC) 
• R-Value Work: 
  0.157 (Depositor), 0.157 (DCC) 
• R-Value Observed: 
  0.158 (Depositor) 

Literature

Crystal Structure of S-adenosylmethionine-dependent methyltransferase UmaA from Mycobacterium tuberculosis in complex with a 12-mer PEG

Abendroth, J., Weiss, M.J., Lorimer, D.D., Horanyi, P.S., Edwards, T.E.

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: 34.93 kDa 
• Atom Count: 2,668 
• Modeled Residue Count: 282 
• Deposited Residue Count: 294 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
S-adenosylmethionine-dependent methyltransferase UmaA	A	294	Mycobacterium tuberculosis H37Rv	Mutation(s): 0  Gene Names: umaA, Rv0469, LH57_02505 EC: 2.1.1
UniProt
Find proteins for Q6MX39 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore Q6MX39  Go to UniProtKB:  Q6MX39

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
12P	B [auth A]	DODECAETHYLENE GLYCOL C24 H50 O13 WRZXKWFJEFFURH-UHFFFAOYSA-N
EDO	C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
NO3	D [auth A], E [auth A]	NITRATE ION N O3 NHNBFGGVMKEFGY-UHFFFAOYSA-N
CL	F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free:  0.175 (Depositor), 0.176 (DCC) 
• R-Value Work:  0.157 (Depositor), 0.157 (DCC) 
• R-Value Observed: 0.158 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m37l9u

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.02	α = 90
b = 103.02	β = 90
c = 49.76	γ = 120

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
PHASER	phasing
PARROT	phasing
ARP/wARP	model building
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-02-10 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2021-02-10
  Type: Initial release
  
• Version 1.1: 2024-03-06
  Changes: Data collection, Database references
• Version 1.2: 2025-10-22
  Changes: Structure summary