2UYK

Crystal structure of E. coli TdcF with bound serine

• PDB DOI: https://doi.org/10.2210/pdb2UYK/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Escherichia coli
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2007-04-10 Released: 2007-05-29 
• Deposition Author(s): Burman, J.D., Stevenson, C.E.M., Sawers, R.G., Lawson, D.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.199 
• R-Value Work: 0.155 
• R-Value Observed: 0.157 

Literature

The Crystal Structure of Escherichia Coli Tdcf, a Member of the Highly Conserved Yjgf/Yer057C/Uk114 Family.

Burman, J.D., Stevenson, C.E.M., Sawers, R.G., Lawson, D.M.

(2007) BMC Struct Biol 7: 30

• PubMed: 17506874 
• DOI: https://doi.org/10.1186/1472-6807-7-30
• Primary Citation of Related Structures:  
  2UYJ, 2UYK, 2UYN, 2UYP


• PubMed Abstract: 
  

  The YjgF/YER057c/UK114 family of proteins is widespread in nature, but has as yet no clearly defined biological role. Members of the family exist as homotrimers and are characterised by intersubunit clefts that are delineated by well-conserved residues; these sites are likely to be of functional significance, yet catalytic activity has never been detected for any member of this family. The gene encoding the TdcF protein of E. coli, a YjgF/YER057c/UK114 family member, resides in an operon that strongly suggests a role in the metabolism of 2-ketobutyrate for this protein.

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Organizational Affiliation: 

Department of Biological Chemistry, John Innes Centre, Norwich, UK. [e-mail]

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Macromolecule Content

• Total Structure Weight: 42.31 kDa 
• Atom Count: 3,352 
• Modelled Residue Count: 381 
• Deposited Residue Count: 387 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN TDCF	A, B, C	129	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0AGL2 (Escherichia coli (strain K12)) Explore P0AGL2  Go to UniProtKB:  P0AGL2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SER	D [auth C]	SERINE C3 H7 N O3 MTCFGRXMJLQNBG-REOHCLBHSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
OCS	A, B, C	L-PEPTIDE LINKING	C3 H7 N O5 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.199 
• R-Value Work: 0.155 
• R-Value Observed: 0.157 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.685	α = 90
b = 86.351	β = 90
c = 62.598	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-05-29 
Deposition Author(s): Burman, J.D., Stevenson, C.E.M., Sawers, R.G., Lawson, D.M.

Revision History  

• Version 1.0: 2007-05-29
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description