1Q7E

Crystal Structure of YfdW protein from E. coli


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.156 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of Escherichia coli YfdW, a type III CoA transferase.

Gogos, A.Gorman, J.Shapiro, L.

(2004) Acta Crystallogr.,Sect.D 60: 507-511

  • DOI: 10.1107/S0907444904000034
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Crystal structures are reported for free and coenzyme A (CoA) bound forms of the YfdW protein from Escherichia coli, a representative type III CoA transferase. The structures reveal a two-domain protomer with interdomain connections forming a ring-li ...

    Crystal structures are reported for free and coenzyme A (CoA) bound forms of the YfdW protein from Escherichia coli, a representative type III CoA transferase. The structures reveal a two-domain protomer with interdomain connections forming a ring-like structure with a large central hole. Two protomers associate to form a highly intertwined dimer in which the hole of each ring is filled by the partner molecule. Each protomer binds a single CoA molecule and these CoA-binding sites are distant from one another in the dimer.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biophysics, Columbia University College of Physicians and Surgeons, 630 West 168th Street, New York, NY 10032, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hypothetical protein yfdW
A
428Escherichia coli (strain K12)Gene Names: frc (yfdW)
EC: 2.8.3.16
Find proteins for P69902 (Escherichia coli (strain K12))
Go to UniProtKB:  P69902
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MPD
Query on MPD

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

Download SDF File 
Download CCD File 
A
METHIONINE
C5 H11 N O2 S
FFEARJCKVFRZRR-BYPYZUCNSA-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

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.156 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 92.366α = 90.00
b = 69.605β = 108.63
c = 73.219γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
DENZOdata reduction
SHARPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-09-30
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance