2DER

Cocrystal structure of an RNA sulfuration enzyme MnmA and tRNA-Glu in the initial tRNA binding state

Structural Biology Knowledgebase: 2DER SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.269
  • R-Value Work: 0.219

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2DER

Classification: Transferase / RNA

Total Structure Weight: 134442.17


Macromolecule Entities
Molecule Chains Length Organism Details
tRNA-specific 2-thiouridylase mnmA A, B 380 Escherichia coli EC#: 2.8.1 IUBMB
Gene Name(s): mnmA asuE trmU ycfB b1133 JW1119
Macromolecule Entities
Molecule Chains Length Organism Details
tRNA C, D 76 synthetic

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
SO4
Query on SO4

A, B SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PO4
Query on PO4

A, B, C PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.269
  • R-Value Work: 0.219
  • Space Group: C 1 2 1

Unit Cell:

Length (Å) Angle (°)
a = 225.39 α = 90.00
b = 175.85 β = 101.62
c = 52.97 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2006-02-17
  • Released Date: 2006-08-15
  • Deposition author(s): Numata, T., Ikeuchi, Y., Fukai, S., Suzuki, T., Nureki, O.

Revision History

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