1QU9

1.2 A CRYSTAL STRUCTURE OF YJGF GENE PRODUCT FROM E. COLI

• PDB DOI: https://doi.org/10.2210/pdb1QU9/pdb

• Classification: STRUCTURAL GENOMICS
• Organism(s): Escherichia coli
• Mutation(s): Yes 


• Deposited: 1999-07-07 Released: 1999-12-01 
• Deposition Author(s): Volz, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Work: 0.164 

Literature

A test case for structure-based functional assignment: the 1.2 A crystal structure of the yjgF gene product from Escherichia coli

Volz, K.

(1999) Protein Sci 8: 2428-2437

• PubMed: 10595546 
• DOI: https://doi.org/10.1110/ps.8.11.2428
• Primary Citation of Related Structures:  
  1QU9


• PubMed Abstract: 
  

  The YER057c/YIL051c/YjgF protein family is a set of 24 full-length homologs, each approximately 130 residues in length, and each with no known function or relationship to proteins of known structure. To determine the function of this family, the structure of one member--the YjgF protein from Escherichia coli--was solved and refined at a resolution of 1.2 A. The YjgF molecule is a homotrimer with exact threefold symmetry. Its tertiary and quaternary structures are related to that of Bacillus subtilis chorismate mutase, although their active sites are completely different. The YjgF protein has an active site curiously similar to protein tyrosine phosphatases, including a covalently modified cysteine, but it is unlikely to be functionally related. The lessons learned from this attempt to deduce function from structure may be useful to future projects in structural genomics.

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Organizational Affiliation: 

Department of Microbiology and Immunology, University of Illinois at Chicago, 60612-7344, USA. [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 PISA (software)

Macromolecule Content

• Total Structure Weight: 41.12 kDa 
• Atom Count: 3,321 
• Modelled Residue Count: 381 
• Deposited Residue Count: 384 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
YJGF PROTEIN	A, B, C	128	Escherichia coli	Mutation(s): 1  EC: 3.5.99.10
UniProt
Find proteins for P0AF93 (Escherichia coli (strain K12)) Explore P0AF93  Go to UniProtKB:  P0AF93

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSP	A, B, C	L-PEPTIDE LINKING	C3 H8 N O5 P S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Work: 0.164 
• Space Group: P 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.22	α = 90
b = 72.22	β = 90
c = 72.22	γ = 90

Software Package:

Software Name	Purpose
MLPHARE	phasing
PROFFT	refinement
SMART	data reduction
SAINT	data reduction
SMART	data scaling
SAINT	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-12-01 
Deposition Author(s): Volz, K.

Revision History  

• Version 1.0: 1999-12-01
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-01-31
  Changes: Experimental preparation
• Version 1.4: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary