3CA8

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 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 ydcFA, B266Escherichia coli K-12Mutation(s): 0 
Gene Names: ydcFb1414JW1411
Find proteins for P34209 (Escherichia coli (strain K12))
Explore P34209 
Go to UniProtKB:  P34209
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MPD
Query on MPD

Download CCD File 
A, B
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 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
b = 39.71β = 96.34
c = 122.645γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SHELXDphasing
SOLVEphasing
RESOLVEmodel building
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RESOLVEphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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