6Y21 | pdb_00006y21

Crystal structure of delta466-491 cystathionine beta-synthase from Toxoplasma gondii with L-Cystathionine

• PDB DOI: https://doi.org/10.2210/pdb6Y21/pdb

• Classification: CYTOSOLIC PROTEIN
• Organism(s): Toxoplasma gondii ME49
• Expression System: Toxoplasma gondii ME49
• Mutation(s): No 


• Deposited: 2020-02-14 Released: 2021-02-24 
• Deposition Author(s): Fernandez-Rodriguez, C., Oyenarte, I., Conter, C., Gonzalez-Recio, I., Quintana, I., Martinez-Chantar, M., Astegno, A., Martinez-Cruz, L.A.
• Funding Organization(s): Ministry of Economy and Competitiveness (MINECO)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.60 Å
• R-Value Free: 
  0.290 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.263 (Depositor), 0.260 (DCC) 
• R-Value Observed: 
  0.264 (Depositor) 

Starting Model: experimental

Literature

Cystathionine Beta-synthase from Toxoplasma gondii with PLP-Cystathionine

Fernandez-Rodriguez, C., Oyenarte, I., Conter, C., Gonzalez-Recio, I., Quintana, I., Martinez-Chantar, M., Astegno, A., Martinez-Cruz, L.A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 168.83 kDa 
• Atom Count: 10,787 
• Modeled Residue Count: 1,425 
• Deposited Residue Count: 1,542 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cystathionine beta-synthase	A [auth D], B [auth A], C [auth B]	514	Toxoplasma gondii ME49	Mutation(s): 0  Gene Names: TGME49_259180 EC: 4.2.1.22
UniProt
Find proteins for A0A125YSJ9 (Toxoplasma gondii (strain ATCC 50611 / Me49)) Explore A0A125YSJ9  Go to UniProtKB:  A0A125YSJ9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
P1T (Subject of Investigation/LOI)	D, E [auth A], F [auth B]	2-[({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)AMINO]ACRYLIC ACID C11 H15 N2 O7 P BXUDKFHCAMQSRX-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.60 Å
• R-Value Free:  0.290 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.263 (Depositor), 0.260 (DCC) 
• R-Value Observed: 0.264 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.006	α = 90
b = 83.006	β = 90
c = 421.373	γ = 120

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-02-24 
Deposition Author(s): Fernandez-Rodriguez, C., Oyenarte, I., Conter, C., Gonzalez-Recio, I., Quintana, I., Martinez-Chantar, M., Astegno, A., Martinez-Cruz, L.A.

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Funding Organization	Location	Grant Number
Ministry of Economy and Competitiveness (MINECO)	Spain	BFU2013-47531-R
Ministry of Economy and Competitiveness (MINECO)	Spain	BES-2014-068464
Ministry of Economy and Competitiveness (MINECO)	Spain	BFU2016-77408-R
Ministry of Economy and Competitiveness (MINECO)	Spain	BES-2017-080435

Revision History  

• Version 1.0: 2021-02-24
  Type: Initial release
  
• Version 1.1: 2021-03-31
  Changes: Structure summary
• Version 1.2: 2024-01-24
  Changes: Data collection, Database references, Refinement description