5EPE

Crystal structure of SAM-dependent methyltransferase from Thiobacillus denitrificans in complex with S-Adenosyl-L-homocysteine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.167 
  • R-Value Work: 0.136 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structure of SAM-dependent methyltransferase from Thiobacillus denitrificans in complex with S-Adenosyl-L-homocysteine

LaRowe, C.Shabalin, I.G.Kutner, J.Handing, K.B.Minor, W.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SAM-dependent methyltransferase
A
248Thiobacillus denitrificans (strain ATCC 25259)N/A
Find proteins for Q3SJX0 (Thiobacillus denitrificans (strain ATCC 25259))
Go to UniProtKB:  Q3SJX0
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
SAH
Query on SAH

Download SDF File 
Download CCD File 
A
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 157.536α = 90.00
b = 157.536β = 90.00
c = 157.536γ = 90.00
Software Package:
Software NamePurpose
DMphasing
MLPHAREphasing
HKL-3000phasing
BLU-MAXdata collection
HKL-3000data reduction
SHELXphasing
PDB_EXTRACTdata extraction
REFMACrefinement
HKL-3000data scaling
Cootmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant Number
National Institutes of HealthUnited States--

Revision History 

  • Version 1.0: 2015-11-25
    Type: Initial release
  • Version 1.1: 2015-12-23
    Type: Other
  • Version 1.2: 2016-02-24
    Type: Other
  • Version 1.3: 2017-09-27
    Type: Author supporting evidence, Derived calculations, Refinement description