4OE7 | pdb_00004oe7

Crystal structure of YagE, a KDG aldolase protein, in complex with aldol condensed product of pyruvate and glyoxal

• PDB DOI: https://doi.org/10.2210/pdb4OE7/pdb

• Classification: LYASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-01-12 Released: 2014-12-24 
• Deposition Author(s): Manoj Kumar, P., Baskar, V., Manicka, S., Krishnaswamy, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free: 
  0.233 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.198 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.200 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of YagE, a KDG aldolase protein, in complex with aldol condensed product of pyruvate and glyoxal

Manoj Kumar, P., Baskar, V., Manicka, S., Krishnaswamy, S.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 151.1 kDa 
• Atom Count: 9,434 
• Modeled Residue Count: 1,192 
• Deposited Residue Count: 1,372 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable 2-keto-3-deoxy-galactonate aldolase YagE	A, B, C, D	343	Escherichia coli K-12	Mutation(s): 0  Gene Names: b0268, JW0261, yagE EC: 4.1.2 (PDB Primary Data), 4.1.2.51 (UniProt), 4.1.2.28 (UniProt)
UniProt
Find proteins for P75682 (Escherichia coli (strain K12)) Explore P75682  Go to UniProtKB:  P75682

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GXS	UA [auth D], Y [auth B]	(4R)-4-hydroxy-2,5-dioxopentanoic acid C5 H6 O5 QZKCWTOLHHFWCD-GSVOUGTGSA-N
GXP	TA [auth D], X [auth B]	(4S)-4-hydroxy-2,5-dioxopentanoic acid C5 H6 O5 QZKCWTOLHHFWCD-VKHMYHEASA-N
GOL	AA [auth C], F [auth A], P [auth B], Q [auth B], QA [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
PYR	KA [auth C], N [auth A]	PYRUVIC ACID C3 H4 O3 LCTONWCANYUPML-UHFFFAOYSA-N
EDO	CA [auth C], DA [auth C], E [auth A], EA [auth C], FA [auth C], G [auth A], GA [auth C], HA [auth C], I [auth A], IA [auth C], J [auth A], JA [auth C], K [auth A], L [auth A], LA [auth C], MA [auth D], NA [auth D], O [auth B], OA [auth D], PA [auth D], R [auth B], SA [auth D], T [auth B], U [auth B], V [auth B], W [auth B], Z [auth C]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
GXT	M [auth A]	ethanedial C2 H2 O2 LEQAOMBKQFMDFZ-UHFFFAOYSA-N
MG	BA [auth C], H [auth A], RA [auth D], S [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free:  0.233 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.198 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.200 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 141.24	α = 90
b = 155.14	β = 90
c = 55.58	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-12-24 
Deposition Author(s): Manoj Kumar, P., Baskar, V., Manicka, S., Krishnaswamy, S.

Revision History  

• Version 1.0: 2014-12-24
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Refinement description
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Derived calculations
• Version 2.1: 2024-11-27
  Changes: Structure summary