1Q6Y

Hypothetical protein YfdW from E. coli bound to Coenzyme A

• PDB DOI: https://doi.org/10.2210/pdb1Q6Y/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2003-08-14 Released: 2003-09-30 
• Deposition Author(s): Gogos, A., Gorman, J., Shapiro, L., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free: 0.200 
• R-Value Work: 0.160 

Literature

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

Gogos, A., Gorman, J., Shapiro, L.

(2004) Acta Crystallogr D Biol Crystallogr 60: 507-511

• PubMed: 14993676 
• DOI: https://doi.org/10.1107/S0907444904000034
• Primary Citation of Related Structures:  
  1PQY, 1Q6Y, 1Q7E


• 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-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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content

• Total Structure Weight: 48.83 kDa 
• Atom Count: 3,592 
• Modelled Residue Count: 417 
• Deposited Residue Count: 428 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein yfdW	A	428	Escherichia coli	Mutation(s): 0  Gene Names: YFDW
UniProt
Find proteins for P69902 (Escherichia coli (strain K12)) Explore P69902  Go to UniProtKB:  P69902

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
COA	B [auth A]	COENZYME A C21 H36 N7 O16 P3 S RGJOEKWQDUBAIZ-IBOSZNHHSA-N
MPD	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free: 0.200 
• R-Value Work: 0.160 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.117	α = 90
b = 66.779	β = 108.73
c = 73.049	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
REFMAC	refinement
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-09-30 
Deposition Author(s): Gogos, A., Gorman, J., Shapiro, L., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2003-09-30
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2021-02-03
  Changes: Database references, Derived calculations, Structure summary
• Version 1.4: 2023-08-16
  Changes: Data collection, Database references, Refinement description