8TXA

Apo Structure of (N1G37) tRNA Methyltransferase from Mycobacterium marinum

• PDB DOI: https://doi.org/10.2210/pdb8TXA/pdb

• Classification: TRANSFERASE
• Organism(s): Mycobacterium marinum
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-08-23 Released: 2024-04-10 
• Deposition Author(s): Balsamo, A., Bruno, C., Edele, C., Fabian, T., Jannotta, R., Lee, R., Schryver, D., Warsaw, J., Warsaw, L., Stojanoff, V., Battaile, K., Perez, A., Bolen, R.
• Funding Organization(s): Brookhaven National Laboratory (BNL)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.59 Å
• R-Value Free: 0.224 
• R-Value Work: 0.188 
• R-Value Observed: 0.189 

Literature

Apo Structure of (N1G37) tRNA Methyltransferase from Mycobacterium marinum

Balsamo, A., Bruno, C., Edele, C., Fabian, T., Jannotta, R., Lee, R., Schryver, D., Warsaw, J., Warsaw, L., Stojanoff, V., Battaile, K., Perez, A., Bolen, R.

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 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 110.72 kDa 
• Atom Count: 6,420 
• Modelled Residue Count: 787 
• Deposited Residue Count: 1,000 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
tRNA (guanine-N(1)-)-methyltransferase	A, B, C, D	250	Mycobacterium marinum	Mutation(s): 0  Gene Names: trmD
UniProt
Find proteins for A0A2Z5YCU9 (Mycobacterium marinum) Explore A0A2Z5YCU9  Go to UniProtKB:  A0A2Z5YCU9

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.59 Å
• R-Value Free: 0.224 
• R-Value Work: 0.188 
• R-Value Observed: 0.189 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.94	α = 97.05
b = 60.797	β = 111.99
c = 68.072	γ = 100.69

Software Package:

Software Name	Purpose
BUSTER	refinement
autoPROC	data processing
PHENIX	phasing
XDS	data reduction
Aimless	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-04-10 
Deposition Author(s): Balsamo, A., Bruno, C., Edele, C., Fabian, T., Jannotta, R., Lee, R., Schryver, D., Warsaw, J., Warsaw, L., Stojanoff, V., Battaile, K., Perez, A., Bolen, R.

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Funding Organization	Location	Grant Number
Brookhaven National Laboratory (BNL)	United States	DE-SC0012704

Revision History  

• Version 1.0: 2024-04-10
  Type: Initial release