6EZL | pdb_00006ezl

Crystal structure of aspartate aminotransferase from Trypanosoma cruzi at 2.07 Angstrom resolution

PDB DOI: https://doi.org/10.2210/pdb6EZL/pdb

Classification: TRANSFERASE
Organism(s): Trypanosoma cruzi strain CL Brener
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2017-11-15 Released: 2018-12-12
Deposition Author(s): Jagoe, W.N., Khan, A.R.
Funding Organization(s): Science Foundation Ireland

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.07 Å
R-Value Free:
0.229 (Depositor), 0.230 (DCC)
R-Value Work:
0.180 (Depositor), 0.180 (DCC)
R-Value Observed:
0.181 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Structure of aspartate aminotransferase from Trypanosoma Cruzi at 2.07 Angstrom resolution

Jagoe, W.N., Barry, P.J.G., Nolan, D.P., Khan, A.R.

To be published.

Macromolecule Content

Total Structure Weight: 90.24 kDa
Atom Count: 6,635
Modeled Residue Count: 784
Deposited Residue Count: 808
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aspartate aminotransferase	A, B	404	Trypanosoma cruzi strain CL Brener	Mutation(s): 0 Gene Names: Tc00.1047053503841.70 EC: 2.6.1.1
UniProt
Find proteins for Q4D080 (Trypanosoma cruzi (strain CL Brener)) Explore Q4D080 Go to UniProtKB: Q4D080
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q4D080
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PLP Query on PLP Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	PYRIDOXAL-5'-PHOSPHATE C₈ H₁₀ N O₆ P NGVDGCNFYWLIFO-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.07 Å
R-Value Free: 0.229 (Depositor), 0.230 (DCC)
R-Value Work: 0.180 (Depositor), 0.180 (DCC)
R-Value Observed: 0.181 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.495	α = 90
b = 59.086	β = 112.64
c = 139.015	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2018-12-12

Deposition Author(s):

Funding Organization	Location	Grant Number
Science Foundation Ireland	Ireland	12/1A/1239

Revision History (Full details and data files)

Version 1.0: 2018-12-12
Type: Initial release
Version 1.1: 2024-01-17
Changes: Data collection, Database references, Refinement description

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.