6PNZ

The structure of the Aspartate Transcarbamoylase trimer from Staphylococcus aureus complexed with PALA at 2.27 Resolution.

PDB DOI: https://doi.org/10.2210/pdb6PNZ/pdb

Classification: TRANSFERASE
Organism(s): Staphylococcus aureus subsp. aureus COL
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2019-07-03 Released: 2020-07-08
Deposition Author(s): Edwards, B.F.P., Evans, D.R., Patel, C.
Funding Organization(s): American Heart Association

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.27 Å
R-Value Free: 0.208
R-Value Work: 0.181
R-Value Observed: 0.182

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

The structure of the Aspartate Transcarbamoylase trimer from Staphylococcus aureus complexed with PALA at 2.27 Resolution.

Edwards, B.F.P., Evans, D.R., Patel, C.

To be published.

Macromolecule Content

Total Structure Weight: 100.66 kDa
Atom Count: 7,238
Modelled Residue Count: 879
Deposited Residue Count: 879
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 carbamoyltransferase	A, B, C	293	Staphylococcus aureus subsp. aureus COL	Mutation(s): 0 Gene Names: pyrB, SACOL1212 EC: 2.1.3.2
UniProt
Find proteins for Q5HGN2 (Staphylococcus aureus (strain COL)) Explore Q5HGN2 Go to UniProtKB: Q5HGN2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5HGN2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PAL (Subject of Investigation/LOI) Query on PAL Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth B] SDF format, chain F [auth C] MOL2 format, chain D [auth A] MOL2 format, chain E [auth B] MOL2 format, chain F [auth C]	D [auth A], E [auth B], F [auth C]	N-(PHOSPHONACETYL)-L-ASPARTIC ACID C₆ H₁₀ N O₈ P ZZKNRXZVGOYGJT-VKHMYHEASA-N		Interactions Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.27 Å
R-Value Free: 0.208
R-Value Work: 0.181
R-Value Observed: 0.182
Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.998	α = 90
b = 111.998	β = 90
c = 151.358	γ = 120

Software Package:

Software Name	Purpose
REFMAC	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: 2020-07-08

Deposition Author(s):

Edwards, B.F.P.

Funding Organization	Location	Grant Number
American Heart Association	United States	17PRE33660545

Revision History (Full details and data files)

Version 1.0: 2020-07-08
Type: Initial release
Version 1.1: 2023-10-11
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.