2HMA | pdb_00002hma

The Crystal Structure of tRNA (5-Methylaminomethyl-2-Thiouridylate)-Methyltransferase TrmU from Streptococcus pneumoniae

• PDB DOI: https://doi.org/10.2210/pdb2HMA/pdb

• Classification: TRANSFERASE
• Organism(s): Streptococcus pneumoniae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2006-07-11 Released: 2006-08-08 
• Deposition Author(s): Kim, Y., Zhou, M., Abdullah, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.41 Å
• R-Value Free: 
  0.217 (Depositor), 0.206 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.184 (DCC) 
• R-Value Observed: 
  0.193 (Depositor) 

Literature

The Crystal Structure of tRNA (5-Methylaminomethyl-2-Thiouridylate)-Methyltransferase TrmU from Streptococcus pneumoniae

Kim, Y., Zhou, M., Abdullah, J., Joachimiak, A.

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.

Macromolecule Content 

• Total Structure Weight: 42.99 kDa 
• Atom Count: 3,313 
• Modeled Residue Count: 364 
• Deposited Residue Count: 376 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase	A	376	Streptococcus pneumoniae	Mutation(s): 12  Gene Names: trmU EC: 2.1.1.61 (PDB Primary Data), 2.8.1.13 (UniProt)
UniProt
Find proteins for Q97T38 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)) Explore Q97T38  Go to UniProtKB:  Q97T38

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAM	C [auth A]	S-ADENOSYLMETHIONINE C15 H22 N6 O5 S MEFKEPWMEQBLKI-FCKMPRQPSA-N
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.41 Å
• R-Value Free:  0.217 (Depositor), 0.206 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.184 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.319	α = 90
b = 93.319	β = 90
c = 157.018	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
HKL-3000	phasing
SHELXE	model building
SOLVE	phasing
RESOLVE	phasing
ARP/wARP	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-08-08 
Deposition Author(s): Kim, Y., Zhou, M., Abdullah, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2006-08-08
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary