5ZW4

Crystal structure of tRNA bound TrmR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Identification of a novel tRNA wobble uridine modifying activity in the biosynthesis of 5-methoxyuridine

Ryu, H.Grove, T.L.Almo, S.C.Kim, J.

(2018) Nucleic Acids Res. --: --


Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Putative O-methyltransferase YrrM
A
225Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: yrrM
EC: 2.1.1.-
Find proteins for O32036 (Bacillus subtilis (strain 168))
Go to UniProtKB:  O32036
Entity ID: 2
MoleculeChainsLengthOrganism
RNA (5'-R(*CP*CP*UP*GP*CP*UP*UP*UP*GP*CP*AP*CP*GP*CP*AP*GP*G)-3')D17Bacillus subtilis subsp. subtilis str. 168
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
SAM
Query on SAM

Download SDF File 
Download CCD File 
A
S-ADENOSYLMETHIONINE
C15 H22 N6 O5 S
MEFKEPWMEQBLKI-FCKMPRQPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.193 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 64.982α = 90.00
b = 64.982β = 90.00
c = 126.680γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
REFMACrefinement
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation (Korea)Korea, Republic Of2016R1D1A1B03930716

Revision History 

  • Version 1.0: 2018-07-11
    Type: Initial release