2ZM5

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

Structural Biology Knowledgebase: 2ZM5 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.270
  • R-Value Work: 0.240

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2ZM5

Classification: TRANSFERASE / RNA

Total Structure Weight: 120106.72


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
Macromolecule Entities
Molecule Chains Length Organism Details
tRNA(Phe) C, D 76 Escherichia coli

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
MG
Query on MG

C, D MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
MSE
Query on MSE
A, B L-PEPTIDE LINKING C5 H11 N O2 Se MET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.270
  • R-Value Work: 0.240
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 88.20 α = 90.00
b = 89.40 β = 90.00
c = 150.80 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2008-04-11
  • Released Date: 2009-04-14
  • Deposition author(s): Sakai, J., Yao, M., Chimnaronk, S., Tanaka, I.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4