3KY7 | pdb_00003ky7

2.35 Angstrom resolution crystal structure of a putative tRNA (guanine-7-)-methyltransferase (trmD) from Staphylococcus aureus subsp. aureus MRSA252

• PDB DOI: https://doi.org/10.2210/pdb3KY7/pdb

• Classification: TRANSFERASE
• Organism(s): Staphylococcus aureus subsp. aureus MRSA252
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-12-04 Released: 2009-12-22 
• Deposition Author(s): Halavaty, A.S., Minasov, G., Winsor, J., Dubrovska, I., Shuvalova, L., See, R., Zoraghi, R., Reiner, N., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 
  0.255 (Depositor), 0.267 (DCC) 
• R-Value Work: 
  0.209 (Depositor), 0.226 (DCC) 
• R-Value Observed: 
  0.211 (Depositor) 

Literature

2.35 Angstrom resolution crystal structure of a putative tRNA (guanine-7-)-methyltransferase (trmD) from Staphylococcus aureus subsp. aureus MRSA252

Halavaty, A.S., Minasov, G., Winsor, J., Dubrovska, I., Shuvalova, L., See, R., Zoraghi, R., Reiner, N., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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)

Macromolecule Content 

• Total Structure Weight: 30.85 kDa 
• Atom Count: 1,945 
• Modeled Residue Count: 229 
• Deposited Residue Count: 269 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
tRNA (guanine-N(1)-)-methyltransferase	A	269	Staphylococcus aureus subsp. aureus MRSA252	Mutation(s): 0  Gene Names: SAR1216, trmD EC: 2.1.1.31 (PDB Primary Data), 2.1.1.228 (UniProt)
UniProt
Find proteins for Q6GHJ5 (Staphylococcus aureus (strain MRSA252)) Explore Q6GHJ5  Go to UniProtKB:  Q6GHJ5

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
OCS	A	L-PEPTIDE LINKING	C3 H7 N O5 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free:  0.255 (Depositor), 0.267 (DCC) 
• R-Value Work:  0.209 (Depositor), 0.226 (DCC) 
• R-Value Observed: 0.211 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m33ky7

Space Group: P 4₃ 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 125.176	α = 90
b = 125.176	β = 90
c = 125.176	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
HKL-3000	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-12-22 
Deposition Author(s): Halavaty, A.S., Minasov, G., Winsor, J., Dubrovska, I., Shuvalova, L., See, R., Zoraghi, R., Reiner, N., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2009-12-22
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2025-03-26
  Changes: Data collection, Database references, Derived calculations, Structure summary