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 

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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Probable 2-keto-3-deoxy-galactonate aldolase YagE
A, B, C, D
343Escherichia coli (strain K12)Gene Names: yagE
EC: 4.1.2.-
Find proteins for P75682 (Escherichia coli (strain K12))
Go to UniProtKB:  P75682
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PYR
Query on PYR

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A, C
PYRUVIC ACID
C3 H4 O3
LCTONWCANYUPML-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

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A, B, C, D
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

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A, B, C, D
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
GXT
Query on GXT

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A
ethanedial
C2 H2 O2
LEQAOMBKQFMDFZ-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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A, B, C, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
GXP
Query on GXP

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B, D
(4S)-4-hydroxy-2,5-dioxopentanoic acid
C5 H6 O5
QZKCWTOLHHFWCD-VKHMYHEASA-N
 Ligand Interaction
GXS
Query on GXS

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Download CCD File 
B, D
(4R)-4-hydroxy-2,5-dioxopentanoic acid
C5 H6 O5
QZKCWTOLHHFWCD-GSVOUGTGSA-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 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 141.240α = 90.00
b = 155.140β = 90.00
c = 55.580γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
PHASERphasing
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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