2HLN

L-asparaginase from Erwinia carotovora in complex with glutamic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.222 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Three-dimensional structures of L-asparaginase from Erwinia carotovora complexed with aspartate and glutamate.

Kravchenko, O.V.Kislitsin, Y.A.Popov, A.N.Nikonov, S.V.Kuranova, I.P.

(2008) Acta Crystallogr D Biol Crystallogr 64: 248-256

  • DOI: https://doi.org/10.1107/S0907444907065766
  • Primary Citation of Related Structures:  
    2GVN, 2HLN

  • PubMed Abstract: 

    The crystal structures of Erwinia carotovora L-asparaginase complexed with L-aspartate and L-glutamate were determined at 1.9 and 2.2 A, respectively, using the molecular-replacement method and were refined to R factors of about 21% in both cases. The positions of the ligands in the active site were located. A comparison of the new structures with the known structures of Escherichia coli L-asparaginase and Er. chrysanthemi L-asparaginase was performed. It was found that the arrangement of the ligands practically coincides in all three enzymes. The peculiarities of the quaternary structure of the enzyme, the possible role of water molecules in the enzyme action and the conformational changes during the catalyzed reaction are discussed.


  • Organizational Affiliation

    Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
L-asparaginase327Pectobacterium atrosepticumMutation(s): 0 
Gene Names: lanS
EC: 3.5.1.1
UniProt
Find proteins for Q7WWK9 (Pectobacterium atrosepticum)
Explore Q7WWK9 
Go to UniProtKB:  Q7WWK9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7WWK9
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GLU
Query on GLU

Download Ideal Coordinates CCD File 
AA [auth K]
FA [auth L]
M [auth A]
O [auth B]
Q [auth E]
AA [auth K],
FA [auth L],
M [auth A],
O [auth B],
Q [auth E],
R [auth F],
S [auth C],
U [auth D],
V [auth G],
X [auth H],
Y [auth I],
Z [auth J]
GLUTAMIC ACID
C5 H9 N O4
WHUUTDBJXJRKMK-VKHMYHEASA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
BA [auth K]
CA [auth K]
DA [auth K]
EA [auth K]
N [auth A]
BA [auth K],
CA [auth K],
DA [auth K],
EA [auth K],
N [auth A],
P [auth B],
T [auth C],
W [auth G]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.222 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.107α = 90
b = 123.675β = 90.92
c = 197.454γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-07-17
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2016-02-24
    Changes: Database references
  • Version 1.4: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description