1MXI

Structure of YibK from Haemophilus influenzae (HI0766): a Methyltransferase with a Cofactor Bound at a Site Formed by a Knot

Structural Biology Knowledgebase: 1MXI SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.254
  • R-Value Work: 0.196

Literature

Macromolecules
Sequence Display for 1MXI

Classification: TRANSFERASE

Total Structure Weight: 18938.86

Macromolecule Entities
Molecule Chains Length Organism Details
Hypothetical tRNA/rRNA methyltransferase HI0766 A 160 Haemophilus influenzae EC#: 2.1.1.207 IUBMB
Gene Name(s): trmL HI_0766
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
IOD
Query on IOD

A IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.254
  • R-Value Work: 0.196
  • Space Group: P 41 21 2

Unit Cell:

Length (Å) Angle (°)
a = 40.80 α = 90.00
b = 40.80 β = 90.00
c = 165.80 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2002-10-02
  • Released Date: 2003-02-25
  • Deposition author(s): Lim, K., Zhang, H., Tempczyk, A., Bonander, N., Toedt, J., Howard, A., Eisenstein, E., Herzberg, O., Structure 2 Function Project (S2F)

Revision History

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