2ZXU

Crystal structure of tRNA modification enzyme MiaA in the complex with tRNA(Phe) and DMASPP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.281
  • R-Value Work: 0.237

Literature

Macromolecules
Sequence Display for 2ZXU

Classification: TRANSFERASE / RNA

Total Structure Weight: 119956.66


Macromolecule Entities
Molecule Chains Length Organism Details
tRNA delta(2)-isopentenylpyrophosphate transferase A, B 316 Escherichia coli EC#: 2.5.1.75 IUBMB
Gene Name(s): miaA trpX b4171 JW4129
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
tRNA(Phe) C, D 76 Escherichia coli

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
DST
Query on DST

A, B DIMETHYLALLYL S-THIOLODIPHOSPHATE
C5 H14 O6 P2 S
UWSFTDFHOGCIEL-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A, B, C, D MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.281
  • R-Value Work: 0.237
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 88.30 α = 90.00
b = 90.00 β = 90.00
c = 150.50 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2009-01-07
  • Released Date: 2009-05-26
  • Deposition author(s): Sakai, J., Yao, M., Chimnaronk, S., Tanaka, I.

Revision History

  • Version 1_0: 2009-05-26

    Type: Initial release

  • Version 1_1: 2011-07-13

    Type: Version format compliance