4OE7

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


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.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Probable 2-keto-3-deoxy-galactonate aldolase YagEA, B, C, D343Escherichia coli K-12Mutation(s): 0 
Gene Names: b0268JW0261yagE
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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GXS
Query on GXS

Download Ideal Coordinates CCD File 
UA [auth D], Y [auth B](4R)-4-hydroxy-2,5-dioxopentanoic acid
C5 H6 O5
QZKCWTOLHHFWCD-GSVOUGTGSA-N
 Ligand Interaction
GXP
Query on GXP

Download Ideal Coordinates CCD File 
TA [auth D], X [auth B](4S)-4-hydroxy-2,5-dioxopentanoic acid
C5 H6 O5
QZKCWTOLHHFWCD-VKHMYHEASA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
AA [auth C], F [auth A], P [auth B], Q [auth B], QA [auth D]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
PYR
Query on PYR

Download Ideal Coordinates CCD File 
KA [auth C], N [auth A]PYRUVIC ACID
C3 H4 O3
LCTONWCANYUPML-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
CA [auth C] , DA [auth C] , E [auth A] , EA [auth C] , FA [auth C] , G [auth A] , GA [auth C] , HA [auth C] , 
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
 Ligand Interaction
GXT
Query on GXT

Download Ideal Coordinates CCD File 
M [auth A]ethanedial
C2 H2 O2
LEQAOMBKQFMDFZ-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
BA [auth C], H [auth A], RA [auth D], S [auth B]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 141.24α = 90
b = 155.14β = 90
c = 55.58γ = 90
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-12-24
    Type: Initial release
  • Version 1.1: 2017-11-22
    Changes: Refinement description