1O7J

Atomic resolution structure of Erwinia chrysanthemi L-asparaginase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.00 Å
  • R-Value Free: 0.128 
  • R-Value Observed: 0.110 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Atomic Resolution Structure of Erwinia Chrysanthemi L-Asparaginase

Lubkowski, J.Dauter, M.Aghaiypour, K.Wlodawer, A.Dauter, Z.

(2003) Acta Crystallogr D Biol Crystallogr 59: 84

  • DOI: 10.1107/s0907444902019443
  • Primary Citation of Related Structures:  
    1O7J

  • PubMed Abstract: 
  • An X-ray structure of L-asparaginase from Erwinia chrysanthemi (ErA) has been refined at 1 A resolution to an R factor of below 0.1, using data collected on a synchrotron source. With four molecules of the enzyme consisting of 327 amino acids each, this crystal contains one of the largest asymmetric units of a protein refined to date at atomic resolution ...

    An X-ray structure of L-asparaginase from Erwinia chrysanthemi (ErA) has been refined at 1 A resolution to an R factor of below 0.1, using data collected on a synchrotron source. With four molecules of the enzyme consisting of 327 amino acids each, this crystal contains one of the largest asymmetric units of a protein refined to date at atomic resolution. Previously, structures of ErA and of related enzymes from other bacterial sources have been refined at resolutions not exceeding 1.7 A; thus, the present structure represents a very significant improvement in the quality of the available models of these proteins and should provide a good basis for future studies of the conformational variability of proteins, identification of subtle conformational features and corroboration of the stereochemical libraries, amongst other things. L-Asparaginases, which are enzymes that catalyze the hydrolysis of L-asparagine to aspartic acid, have been used for over 30 y as therapeutic agents in the treatment of acute childhood lymphoblastic leukemia, although the details of the enzymatic reaction and substrate specificity have not yet been completely elucidated. This atomic resolution structure is a step in that direction.


    Organizational Affiliation

    Macromolecular Crystallography Laboratory, National Cancer Institute at Frederick, Frederick, MD 21702, USA. jacek@ncifcrf.gov



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
L-ASPARAGINASEA, B, C, D327Dickeya chrysanthemiMutation(s): 4 
Gene Names: ansBasn
EC: 3.5.1.1
UniProt
Find proteins for P06608 (Dickeya chrysanthemi)
Explore P06608 
Go to UniProtKB:  P06608
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
E [auth A], F [auth A], M [auth B], N [auth B], R [auth C], S [auth C], T [auth D], U [auth D]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
G [auth A], V [auth D]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
H [auth A] , I [auth A] , J [auth A] , K [auth A] , L [auth A] , O [auth B] , P [auth B] , Q [auth B] , 
H [auth A],  I [auth A],  J [auth A],  K [auth A],  L [auth A],  O [auth B],  P [auth B],  Q [auth B],  W [auth D],  X [auth D],  Y [auth D],  Z [auth D]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.00 Å
  • R-Value Free: 0.128 
  • R-Value Observed: 0.110 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.38α = 90
b = 90.35β = 91.4
c = 127.59γ = 90
Software Package:
Software NamePurpose
SHELXL-97refinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-12-04
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-05-22
    Changes: Advisory, Data collection, Derived calculations, Other, Refinement description