4IV5

X-ray crystal structure of a putative aspartate carbamoyltransferase from Trypanosoma cruzi

PDB DOI: https://doi.org/10.2210/pdb4IV5/pdb

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

Deposited: 2013-01-22 Released: 2013-04-10
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.238
R-Value Work: 0.191
R-Value Observed: 0.194

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

X-ray crystal structure of a putative aspartate carbamoyltransferase from Trypanosoma cruzi

Fairman, J.W., Abendroth, J.A., Edwards, T.E., Lorimer, D.

To be published.

Macromolecule Content

Total Structure Weight: 222.79 kDa
Atom Count: 14,420
Modelled Residue Count: 1,779
Deposited Residue Count: 2,004
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aspartate carbamoyltransferase, putative	A, B, C, D, E A, B, C, D, E, F	334	Trypanosoma cruzi strain CL Brener	Mutation(s): 0 Gene Names: Tc00.1047053508375.30, Tc00.1047053511923.110 EC: 2.1.3.2
UniProt
Find proteins for Q4D3W3 (Trypanosoma cruzi (strain CL Brener)) Explore Q4D3W3 Go to UniProtKB: Q4D3W3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q4D3W3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth B] SDF format, chain L [auth C] SDF format, chain P [auth D] SDF format, chain Q [auth E] SDF format, chain V [auth F] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain L [auth C] MOL2 format, chain P [auth D] MOL2 format, chain Q [auth E] MOL2 format, chain V [auth F] mmCIF format, chain G [auth A] mmCIF format, chain J [auth B] mmCIF format, chain L [auth C] mmCIF format, chain P [auth D] mmCIF format, chain Q [auth E] mmCIF format, chain V [auth F]	G [auth A] J [auth B] L [auth C] P [auth D] Q [auth E] G [auth A], J [auth B], L [auth C], P [auth D], Q [auth E], V [auth F]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain P [auth D] Focus chain Q [auth E] Focus chain V [auth F] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain P [auth D] Focus chain Q [auth E] Focus chain V [auth F]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain R [auth E] MOL2 format, chain R [auth E] mmCIF format, chain R [auth E]	R [auth E]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain R [auth E] Interactions & Density Focus chain R [auth E]
UNX Query on UNX Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain K [auth B] SDF format, chain M [auth C] SDF format, chain N [auth C] SDF format, chain O [auth C] SDF format, chain S [auth E] SDF format, chain T [auth E] SDF format, chain U [auth E] SDF format, chain W [auth F] SDF format, chain X [auth F] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain K [auth B] MOL2 format, chain M [auth C] MOL2 format, chain N [auth C] MOL2 format, chain O [auth C] MOL2 format, chain S [auth E] MOL2 format, chain T [auth E] MOL2 format, chain U [auth E] MOL2 format, chain W [auth F] MOL2 format, chain X [auth F] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain K [auth B] mmCIF format, chain M [auth C] mmCIF format, chain N [auth C] mmCIF format, chain O [auth C] mmCIF format, chain S [auth E] mmCIF format, chain T [auth E] mmCIF format, chain U [auth E] mmCIF format, chain W [auth F] mmCIF format, chain X [auth F]	H [auth A] I [auth A] K [auth B] M [auth C] N [auth C] H [auth A], I [auth A], K [auth B], M [auth C], N [auth C], O [auth C], S [auth E], T [auth E], U [auth E], W [auth F], X [auth F]	UNKNOWN ATOM OR ION X		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C] Focus chain S [auth E] Focus chain T [auth E] Focus chain U [auth E] Focus chain W [auth F] Focus chain X [auth F] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C] Focus chain S [auth E] Focus chain T [auth E] Focus chain U [auth E] Focus chain W [auth F] Focus chain X [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.238
R-Value Work: 0.191
R-Value Observed: 0.194
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.98	α = 90
b = 134.55	β = 90
c = 159.46	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2013-04-10

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2013-04-10
Type: Initial release
Version 1.1: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description