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)  |  3D 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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP75682
Protein Feature View
Expand
  • 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

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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

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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

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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],
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

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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