5CO4 | pdb_00005co4

Structural insights into the 2-OH methylation of C/U34 on tRNA

• PDB DOI: https://doi.org/10.2210/pdb5CO4/pdb

• Classification: TRANSFERASE
• Organism(s): Thermus thermophilus HB27
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-07-19 Released: 2016-07-20 
• Deposition Author(s): Xie, W., Pang, P., Wang, Z.
• Funding Organization(s): Guangdong Innovative Research Team Program

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.200 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.173 (Depositor), 0.173 (DCC) 
• R-Value Observed: 
  0.174 (Depositor) 

Starting Model: experimental

Literature

Structural insights into the 2-OH methylation of C34 or U34 on tRNA

Xie, W., Pang, P., Wang, Z.

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: 40.8 kDa 
• Atom Count: 2,790 
• Modeled Residue Count: 313 
• Deposited Residue Count: 356 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative tRNA (cytidine(34)-2'-O)-methyltransferase	A [auth B], B [auth A]	178	Thermus thermophilus HB27	Mutation(s): 0  Gene Names: TT_C1952 EC: 2.1.1.207
UniProt
Find proteins for Q72G96 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)) Explore Q72G96  Go to UniProtKB:  Q72G96

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MTA	C [auth B], E [auth A]	5'-DEOXY-5'-METHYLTHIOADENOSINE C11 H15 N5 O3 S WUUGFSXJNOTRMR-IOSLPCCCSA-N
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.200 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.173 (Depositor), 0.173 (DCC) 
• R-Value Observed: 0.174 (Depositor) 

Space Group: P 6₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.296	α = 90
b = 95.296	β = 90
c = 61.599	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-07-20 
Deposition Author(s): Xie, W., Pang, P., Wang, Z.

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Funding Organization	Location	Grant Number
Guangdong Innovative Research Team Program	China	2011Y038

Revision History  

• Version 1.0: 2016-07-20
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description