1Q7E | pdb_00001q7e

Crystal Structure of YfdW protein from E. coli

• PDB DOI: https://doi.org/10.2210/pdb1Q7E/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2003-08-18 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: 1.60 Å
• R-Value Free: 
  0.186 (Depositor), 0.189 (DCC) 
• R-Value Work: 
  0.156 (Depositor), 0.158 (DCC) 

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 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: 48.78 kDa 
• Atom Count: 3,687 
• Modeled Residue Count: 410 
• 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): 9  Gene Names: YFDW EC: 2.8.3.16
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
MET	B [auth A], C [auth A]	METHIONINE C5 H11 N O2 S FFEARJCKVFRZRR-BYPYZUCNSA-N
MPD	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.186 (Depositor), 0.189 (DCC) 
• R-Value Work:  0.156 (Depositor), 0.158 (DCC) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.366	α = 90
b = 69.605	β = 108.63
c = 73.219	γ = 90

Software Package:

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

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: 2024-11-20
  Changes: Data collection, Database references, Structure summary