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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.60 Å
R-Value Free:
0.290 (Depositor), 0.288 (DCC)
R-Value Work:
0.263 (Depositor), 0.262 (DCC)
R-Value Observed:
0.264 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

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.

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

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A125YSJ9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
P1T (Subject of Investigation/LOI) Query on P1T Download:Ideal Coordinates CCD File SDF format, chain D SDF format, chain E [auth A] SDF format, chain F [auth B] MOL2 format, chain D MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] mmCIF format, chain D mmCIF format, chain E [auth A] mmCIF format, chain F [auth B]	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		Interactions Focus chain D Focus chain E [auth A] Focus chain F [auth B] Interactions & Density Focus chain D Focus chain E [auth A] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.60 Å
R-Value Free: 0.290 (Depositor), 0.288 (DCC)
R-Value Work: 0.263 (Depositor), 0.262 (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

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2021-02-24

Deposition Author(s):

Fernandez-Rodriguez, C.

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 (Full details and data files)

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