5BP9

Crystal structure of SAM-dependent methyltransferase from Bacteroides fragilis in complex with S-Adenosyl-L-homocysteine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.132 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structure of SAM-dependent methyltransferase fromBacteroides fragilis in complex with S-Adenosyl-L-homocysteine

Gasiorowska, O.A.Shabalin, I.G.Handing, K.B.Cymborowski, M.T.Mason, D.Bonanno, J.Seidel, R.Almo, S.C.Minor, W.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Putative methyltransferase protein
A
281Bacteroides fragilis (strain ATCC 25285 / DSM 2151 / JCM 11019 / NCTC 9343)Mutation(s): 0 
Find proteins for Q5LFK0 (Bacteroides fragilis (strain ATCC 25285 / DSM 2151 / JCM 11019 / NCTC 9343))
Go to UniProtKB:  Q5LFK0
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ETE
Query on ETE

Download SDF File 
Download CCD File 
A
2-{2-[2-2-(METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL
C9 H20 O5
ZNYRFEPBTVGZDN-UHFFFAOYSA-N
 Ligand Interaction
PG4
Query on PG4

Download SDF File 
Download CCD File 
A
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-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 = 41.732α = 90.00
b = 70.660β = 90.00
c = 78.743γ = 90.00
Software Package:
Software NamePurpose
BLU-MAXdata collection
PDB_EXTRACTdata extraction
HKL-3000data reduction
REFMACrefinement
MLPHAREphasing
HKL-3000data scaling
HKL-3000phasing
SHELXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of HealthUnited States--

Revision History 

  • Version 1.0: 2015-06-10
    Type: Initial release
  • Version 1.1: 2017-10-11
    Type: Advisory, Derived calculations, Refinement description, Source and taxonomy