1IM8

Crystal structure of YecO from Haemophilus influenzae (HI0319), a methyltransferase with a bound S-adenosylhomocysteine

Structural Biology Knowledgebase: 1IM8 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.255
  • R-Value Work: 0.186

Literature

Macromolecules
Sequence Display for 1IM8

Classification: TRANSFERASE

Total Structure Weight: 56964.13

Macromolecule Entities
Molecule Chains Length Organism Details
YecO A, B 244 Haemophilus influenzae EC#: 2.1.1 IUBMB
Mutation: M30M, M47M, M93M, M127M, M205M, M237M
Gene Name(s): cmoA HI_0319
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, B S-ADENOSYL-L-HOMOSELENOCYSTEINE
C14 H20 N6 O5 Se
UVSMMLABJBJNGH-WFMPWKQPSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

A, B CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer NGL
 
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: 2.2 Å
  • R-Value Free: 0.255
  • R-Value Work: 0.186
  • Space Group: P 61 2 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 74.97 α = 90.00
b = 74.97 β = 90.00
c = 319.12 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2001-05-10
  • Released Date: 2001-11-07
  • 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
  • 2011-07-13
    Type: Source and taxonomy | Details: Removed strain from scientific name