7MYS | pdb_00007mys

Crystal structure of a tRNA (guanine-N1)-methyltransferase from Acinetobacter baumannii AB5075-UW bound to S-adenosyl homocysteine

• PDB DOI: https://doi.org/10.2210/pdb7MYS/pdb

• Classification: TRANSFERASE
• Organism(s): Acinetobacter baumannii
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2021-05-21 Released: 2021-06-09 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.225 (Depositor), 0.225 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.181 (DCC) 
• R-Value Observed: 
  0.185 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a tRNA (guanine-N1)-methyltransferase from Acinetobacter baumannii AB5075-UW bound to S-adenosyl homocysteine

Edwards, T.E., Abendroth, J., Horanyi, P.S., Lorimer, D.D., Seattle Structural Genomics Center for Infectious Disease (SSGCID)

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 58.62 kDa 
• Atom Count: 3,712 
• Modeled Residue Count: 478 
• Deposited Residue Count: 508 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
tRNA (guanine-N(1)-)-methyltransferase	A, B	254	Acinetobacter baumannii	Mutation(s): 0  Gene Names: trmD, ABC003_01337, ABUW_0322, EA686_14030, FDO31_01140, FJU79_00125, GNY86_14875, HYI42_11650 EC: 2.1.1.228
UniProt
Find proteins for B0V8J1 (Acinetobacter baumannii (strain AYE)) Explore B0V8J1  Go to UniProtKB:  B0V8J1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAH (Subject of Investigation/LOI)	C [auth A], D [auth B]	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.225 (Depositor), 0.225 (DCC) 
• R-Value Work:  0.181 (Depositor), 0.181 (DCC) 
• R-Value Observed: 0.185 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m37mys

Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.96	α = 90
b = 65.96	β = 90
c = 132.59	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-06-09 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2021-06-09
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2025-10-22
  Changes: Data collection, Database references, Structure summary