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: 1.90 Å
  • R-Value Free: 0.167 
  • R-Value Work: 0.136 
  • R-Value Observed: 0.137 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.5 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
SAM-dependent methyltransferaseA248Thiobacillus denitrificans ATCC 25259Mutation(s): 0 
Gene Names: Tbd_1076
EC: 2.1.1
UniProt
Find proteins for Q3SJX0 (Thiobacillus denitrificans (strain ATCC 25259))
Explore Q3SJX0 
Go to UniProtKB:  Q3SJX0
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SAH (Subject of Investigation/LOI)
Query on SAH

Download Ideal Coordinates CCD File 
B [auth A]S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
C [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
AL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 157.536α = 90
b = 157.536β = 90
c = 157.536γ = 90
Software Package:
Software NamePurpose
BLU-MAXdata collection
HKL-3000data scaling
HKL-3000phasing
SHELXphasing
DMphasing
MLPHAREphasing
REFMACrefinement
Cootmodel building
PDB_EXTRACTdata extraction
HKL-3000data reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2015-11-25
    Type: Initial release
  • Version 1.1: 2015-12-23
    Changes: Other
  • Version 1.2: 2016-02-24
    Changes: Other
  • Version 1.3: 2017-09-27
    Changes: Author supporting evidence, Derived calculations, Refinement description
  • Version 1.4: 2018-08-15
    Changes: Data collection, Database references
  • Version 1.5: 2019-12-04
    Changes: Author supporting evidence