7Z35 | pdb_00007z35

Crystal structure of PEX13 SH3 domain of Trypanosoma cruzi

PDB DOI: https://doi.org/10.2210/pdb7Z35/pdb

Classification: PROTEIN TRANSPORT
Organism(s): Trypanosoma cruzi
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-03-01 Released: 2023-03-22
Deposition Author(s): Sonani, R.R., Dubin, G.
Funding Organization(s): Polish National Science Centre, Foundation for Polish Science

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.262 (Depositor), 0.275 (DCC)
R-Value Work:
0.245 (Depositor), 0.252 (DCC)
R-Value Observed:
0.245 (Depositor)

Starting Model: experimental
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This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of PEX13 SH3 domain of Trypanosoma cruzi

Sonani, R.R., Dubin, G.

To be published.

Macromolecule Content

Total Structure Weight: 9 kDa
Atom Count: 447
Modeled Residue Count: 56
Deposited Residue Count: 81
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative peroxin 13	A	81	Trypanosoma cruzi	Mutation(s): 0 Gene Names: C4B63_4g75
UniProt
Find proteins for A0A2V2VYH2 (Trypanosoma cruzi) Explore A0A2V2VYH2 Go to UniProtKB: A0A2V2VYH2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A2V2VYH2
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.262 (Depositor), 0.275 (DCC)
R-Value Work: 0.245 (Depositor), 0.252 (DCC)
R-Value Observed: 0.245 (Depositor)

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.481	α = 90
b = 52.481	β = 90
c = 113.969	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-03-22

Deposition Author(s):

Funding Organization	Location	Grant Number
Polish National Science Centre	Poland	2017/26/M/NZ1/00797
Foundation for Polish Science	Poland	TEAM TECH CORE FACILITY/2017-4/6

Revision History (Full details and data files)

Version 1.0: 2023-03-22
Type: Initial release
Version 1.1: 2024-02-07
Changes: Data collection, Refinement description

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.