6M81

Crystal structure of TylM1 Y14F bound to SAH and dTDP-phenol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.782 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.175 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structural and Functional Characterization of Sulfonium Carbon-Oxygen Hydrogen Bonding in the Deoxyamino Sugar Methyltransferase TylM1.

Fick, R.J.Horowitz, S.McDole, B.G.Clay, M.C.Mehl, R.A.Al-Hashimi, H.M.Scheiner, S.Trievel, R.C.

(2019) Biochemistry --: --


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
dTDP-3-amino-3,6-dideoxy-alpha-D-glucopyranose N,N-dimethyltransferase
A, B, C, D
263Streptomyces fradiaeMutation(s): 1 
Gene Names: tylM1 (tylMI)
EC: 2.1.1.235
Find proteins for P95748 (Streptomyces fradiae)
Go to UniProtKB:  P95748
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SAH
Query on SAH

Download SDF File 
Download CCD File 
A, B, C, D
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
 Ligand Interaction
TLO
Query on TLO

Download SDF File 
Download CCD File 
A, B, C, D
5'-O-[(S)-hydroxy{[(S)-hydroxy(phenoxy)phosphoryl]oxy}phosphoryl]thymidine
thymidine diphosphate phenol
C16 H20 N2 O11 P2
BANJVYKYIQPYKP-BFHYXJOUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.782 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.175 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 73.897α = 90.00
b = 92.353β = 106.44
c = 80.561γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
PDB_EXTRACTdata extraction
PHASERphasing
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (United States)United StatesCHE-1508492

Revision History 

  • Version 1.0: 2019-03-13
    Type: Initial release