3CA8

Crystal structure of Escherichia coli YdcF, an S-adenosyl-L-methionine utilizing enzyme


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The Escherichia coli YdcF binds S-adenosyl-L-methionine and adopts an alpha/beta-fold characteristic of nucleotide-utilizing enzymes.

Chao, K.L.Lim, K.Lehmann, C.Doseeva, V.Howard, A.J.Schwarz, F.P.Herzberg, O.

(2008) Proteins 72: 506-509


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein ydcF
A, B
266Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: ydcF
Find proteins for P34209 (Escherichia coli (strain K12))
Go to UniProtKB:  P34209
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
MPD
Query on MPD

Download SDF File 
Download CCD File 
A, B
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.195 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 64.795α = 90.00
b = 39.710β = 96.34
c = 122.645γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
SHELXDphasing
SOLVEphasing
DENZOdata reduction
HKL-2000data collection
SCALEPACKdata scaling
RESOLVEmodel building
RESOLVEphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-05-06
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Source and taxonomy, Version format compliance