3DXX

Crystal structure of EcTrmB

Structural Biology Knowledgebase: 3DXX SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.227
  • R-Value Work: 0.193

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3DXX

Classification: TRANSFERASE

Total Structure Weight: 24923.63

Macromolecule Entities
Molecule Chains Length Organism Details
tRNA (guanine-N(7)-)-methyltransferase A 218 Escherichia coli EC#: 2.1.1.33 IUBMB
Fragment: UNP residues 33-239
Gene Name(s): trmB trmI yggH b2960 JW2927
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.227
  • R-Value Work: 0.193
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 46.42 α = 90.00
b = 47.01 β = 90.01
c = 58.64 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2008-07-25
  • Released Date: 2009-05-19
  • Deposition author(s): Zhou, H.H., Liu, Q., Gao, Y.X., Teng, M.K., Niu, L.W.

Revision History

  • 2011-07-13
    Type: Source and taxonomy | Details: Removed strain from scientific name
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Flag residual B-value | Details: Tagged residual B temperature factor