6NXC

ECAI(T162A) MUTANT IN COMPLEX WITH CITRATE AT PH 4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.168 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 2him


Literature

Opportunistic complexes of E. coli L-asparaginases with citrate anions.

Lubkowski, J.Chan, W.Wlodawer, A.

(2019) Sci Rep 9: 11070-11070

  • DOI: https://doi.org/10.1038/s41598-019-46432-0
  • Primary Citation of Related Structures:  
    6NX6, 6NX7, 6NX8, 6NX9, 6NXA, 6NXB, 6NXC, 6NXD

  • PubMed Abstract: 

    Active sites of enzymes are highly optimized for interactions with specific substrates, thus binding of opportunistic ligands is usually observed only in the absence of native substrates or products. However, during growth of crystals required for structure determination enzymes are often exposed to conditions significantly divergent from the native ones, leading to binding of unexpected ligands to active sites even in the presence of substrates. Failing to recognize this possibility may lead to incorrect interpretation of experimental results and to faulty conclusions. Here, we present several examples of binding of a citrate anion to the active sites of E. coli L-asparaginases I and II, even in the presence of the native substrate, L-Asn. A part of this report focuses on a comprehensive re-interpretation of structural results published previously for complexes of type I L-asparaginase (EcAI) from E. coli. In two re-refined structures a citrate anion forms an acyl-enzyme reaction intermediate with the catalytic threonine. These results emphasize the importance of careful and critical analysis during interpretation of crystallographic data.


  • Organizational Affiliation

    Macromolecular Crystallography Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA. lubkowsj@mail.nih.gov.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
L-asparaginase 1
A, B, C, D
357Escherichia coli K-12Mutation(s): 1 
Gene Names: ansAb1767JW1756
EC: 3.5.1.1
UniProt
Find proteins for P0A962 (Escherichia coli (strain K12))
Explore P0A962 
Go to UniProtKB:  P0A962
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A962
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CIT (Subject of Investigation/LOI)
Query on CIT

Download Ideal Coordinates CCD File 
DA [auth D],
E [auth A],
N [auth B],
X [auth C]
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
ASN (Subject of Investigation/LOI)
Query on ASN

Download Ideal Coordinates CCD File 
CA [auth D],
M [auth A],
O [auth B],
W [auth C]
ASPARAGINE
C4 H8 N2 O3
DCXYFEDJOCDNAF-REOHCLBHSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
I [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
GA [auth D]
HA [auth D]
K [auth A]
F [auth A],
G [auth A],
GA [auth D],
HA [auth D],
K [auth A],
P [auth B],
Q [auth B],
R [auth B],
V [auth C],
Y [auth C],
Z [auth C]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
AA [auth C]
BA [auth D]
EA [auth D]
FA [auth D]
H [auth A]
AA [auth C],
BA [auth D],
EA [auth D],
FA [auth D],
H [auth A],
J [auth A],
L [auth A],
S [auth B],
T [auth B],
U [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.168 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.524α = 90
b = 89.766β = 117.14
c = 93.29γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-08-07
    Type: Initial release
  • Version 1.1: 2019-11-20
    Changes: Database references