3TFI

DMSP-dependent demethylase from P. ubique - with substrate DMSP

Structural Biology Knowledgebase: 3TFI SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.184
  • R-Value Work: 0.130

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3TFI

Classification: TRANSFERASE

Total Structure Weight: 84276.83

Macromolecule Entities
Molecule Chains Length Organism Details
GcvT-like Aminomethyltransferase protein A, B 369 Candidatus pelagibacter ubique EC#: 2.1.1.269 IUBMB
Gene Name(s): dmdA SAR11_0246
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, B 3-(dimethyl-lambda~4~-sulfanyl)propanoic acid
C5 H12 O2 S
BBSYGEAKHYDEGI-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

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

A, B SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.184
  • R-Value Work: 0.130
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 53.75 α = 90.00
b = 121.99 β = 100.17
c = 59.37 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-08-15
  • Released Date: 2011-12-28
  • Deposition author(s): Schuller, D.J., Reisch, C.R., Moran, M.A., Whitman, W.B., Lanzilotta, W.N.

Revision History

  • 2012-02-29
    Type: Citation | Details: Citation update