4ONV

Crystal structure of YagE, a KDG aldolase protein in complex with 2-Keto-3-deoxy gluconate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.57 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.248 

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Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Crystal structure of YagE, a KDG aldolase protein in complex with 2-Keto-3-deoxy gluconate

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

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Probable 2-keto-3-deoxy-galactonate aldolase YagE
A, B, C, D
343Escherichia coli K-12Mutation(s): 0 
Gene Names: b0268JW0261yagE
EC: 4.1.2
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
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
KDG
Query on KDG

Download Ideal Coordinates CCD File 
AA [auth C],
J [auth A],
JA [auth D],
S [auth B]
2-KETO-3-DEOXYGLUCONATE
C6 H10 O6
WPAMZTWLKIDIOP-WVZVXSGGSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
EA [auth D]
F [auth A]
G [auth A]
GA [auth D]
H [auth A]
EA [auth D],
F [auth A],
G [auth A],
GA [auth D],
H [auth A],
HA [auth D],
I [auth A],
IA [auth D],
O [auth B],
P [auth B],
Q [auth B],
R [auth B],
Y [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
BA [auth D]
CA [auth D]
DA [auth D]
E [auth A]
FA [auth D]
BA [auth D],
CA [auth D],
DA [auth D],
E [auth A],
FA [auth D],
K [auth B],
L [auth B],
M [auth B],
N [auth B],
T [auth C],
U [auth C],
V [auth C],
W [auth C],
X [auth C],
Z [auth C]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.57 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.248 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 141.17α = 90
b = 155.41β = 90
c = 55.51γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-01-14
    Type: Initial release