4EFC | pdb_00004efc

Crystal Structure of Adenylosuccinate Lyase from Trypanosoma Brucei, Tb427tmp.160.5560

• PDB DOI: https://doi.org/10.2210/pdb4EFC/pdb

• Classification: LYASE
• Organism(s): Trypanosoma brucei brucei TREU927
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-03-29 Released: 2013-02-13 
• Deposition Author(s): Wernimont, A.K., Loppnau, P., Osman, K.T., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Robinson, D.A., Wyatt, P.G., Gilbert, I.H., Fairlamb, A.H., Hui, R., Lin, Y.H., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.191 (Depositor), 0.195 (DCC) 
• R-Value Work: 
  0.149 (Depositor), 0.155 (DCC) 
• R-Value Observed: 
  0.151 (Depositor) 

Literature

Crystal Structure of Adenylosuccinate Lyase from Trypanosoma Brucei, Tb427tmp.160.5560

Wernimont, A.K., Loppnau, P., Osman, K.T., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Robinson, D.A., Wyatt, P.G., Gilbert, I.H., Hui, R., Lin, Y.H.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 4 generated by PISA (software)

Biological Assembly 5  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 5 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 107.39 kDa 
• Atom Count: 8,304 
• Modeled Residue Count: 902 
• Deposited Residue Count: 944 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenylosuccinate lyase	A, B	472	Trypanosoma brucei brucei TREU927	Mutation(s): 0  Gene Names: Tb09.160.5560 EC: 4.3.2.2
UniProt
Find proteins for Q38EJ2 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1)) Explore Q38EJ2  Go to UniProtKB:  Q38EJ2

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AMP	C [auth A], G [auth B]	ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N
EDO	E [auth A], H [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG	D [auth A], F [auth A], I [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA	J [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.191 (Depositor), 0.195 (DCC) 
• R-Value Work:  0.149 (Depositor), 0.155 (DCC) 
• R-Value Observed: 0.151 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.768	α = 90
b = 140.744	β = 90
c = 60.403	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-02-13 
Deposition Author(s): Wernimont, A.K., Loppnau, P., Osman, K.T., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Robinson, D.A., Wyatt, P.G., Gilbert, I.H., Fairlamb, A.H., Hui, R., Lin, Y.H., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2013-02-13
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description
• Version 1.2: 2024-02-28
  Changes: Data collection, Database references, Derived calculations