4PTN

Crystal Structure of YagE, a KDG aldolase protein in complex with Magnesium cation coordinated L-glyceraldehyde


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.176 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Crystal structure of YagE, a putative DHDPS-like protein from Escherichia coli K12.

Manicka, S.Peleg, Y.Unger, T.Albeck, S.Dym, O.Greenblatt, H.M.Bourenkov, G.Lamzin, V.Krishnaswamy, S.Sussman, J.L.

(2008) Proteins 71: 2102-2108


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 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download Ideal Coordinates CCD File 
M [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
GXV
Query on GXV

Download Ideal Coordinates CCD File 
G [auth A], N [auth B], T [auth C], X [auth D]L-glyceraldehyde
C3 H6 O3
MNQZXJOMYWMBOU-GSVOUGTGSA-N
 Ligand Interaction
PYR
Query on PYR

Download Ideal Coordinates CCD File 
P [auth B], Z [auth D]PYRUVIC ACID
C3 H4 O3
LCTONWCANYUPML-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
E [auth A] , F [auth A] , I [auth B] , J [auth B] , K [auth B] , L [auth B] , Q [auth C] , R [auth C] , 
E [auth A],  F [auth A],  I [auth B],  J [auth B],  K [auth B],  L [auth B],  Q [auth C],  R [auth C],  S [auth C],  V [auth D],  W [auth D]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.176 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 141.2α = 90
b = 155.07β = 90
c = 55.4γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-12-03
    Type: Initial release
  • Version 2.0: 2020-07-08
    Changes: Atomic model, Database references, Derived calculations, Structure summary