6ZFW | pdb_00006zfw

X-ray structure of the soluble N-terminal domain of T. cruzi PEX-14

• PDB DOI: https://doi.org/10.2210/pdb6ZFW/pdb

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


• Deposited: 2020-06-18 Released: 2020-12-09 
• Deposition Author(s): Softley, C.A., Ostertag, M.O., Sattler, M., Popowicz, G.P.
• Funding Organization(s): H2020 Marie Curie Actions of the European Commission

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free: 
  0.206 (Depositor), 0.211 (DCC) 
• R-Value Work: 
  0.171 (Depositor), 0.174 (DCC) 
• R-Value Observed: 
  0.173 (Depositor) 

Starting Model: experimental

Literature

Deep learning model predicts water interaction sites on the surface of proteins using limited-resolution data.

Zaucha, J., Softley, C.A., Sattler, M., Frishman, D., Popowicz, G.M.

(2020) Chem Commun (Camb) 56: 15454-15457

• PubMed: 33237041 
• DOI: https://doi.org/10.1039/d0cc04383d
• Primary Citation Related Structures: 
  6ZFW


• PubMed Abstract: 
  

  We develop a residual deep learning model, hotWater (https://pypi.org/project/hotWater/), to identify key water interaction sites on proteins for binding models and drug discovery. This is tested on new crystal structures, as well as cryo-EM and NMR structures from the PDB and in crystallographic refinement with promising results.

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Organizational Affiliation: 
• Department of Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität München, Maximus-von-Imhof-Forum 3, 85354 Freising, Germany. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors.

Biological Assembly 5  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 5 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 40.03 kDa 
• Atom Count: 3,253 
• Modeled Residue Count: 345 
• Deposited Residue Count: 350 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peroxin-14	A, B, C, D, E	70	Trypanosoma cruzi	Mutation(s): 0  Gene Names: C3747_80g13
UniProt
Find proteins for Q4D1H5 (Trypanosoma cruzi (strain CL Brener)) Explore Q4D1H5  Go to UniProtKB:  Q4D1H5

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	G [auth A], I [auth C], J [auth C], L [auth E]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
BME	F [auth A], H [auth C], K [auth D]	BETA-MERCAPTOETHANOL C2 H6 O S DGVVWUTYPXICAM-UHFFFAOYSA-N
ACT	M [auth E]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free:  0.206 (Depositor), 0.211 (DCC) 
• R-Value Work:  0.171 (Depositor), 0.174 (DCC) 
• R-Value Observed: 0.173 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.688	α = 90
b = 117.382	β = 109.235
c = 51.301	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Coot	model building
XDS	data reduction
XSCALE	data scaling
REFMAC	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-12-09 
Deposition Author(s): Softley, C.A., Ostertag, M.O., Sattler, M., Popowicz, G.P.

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Funding Organization	Location	Grant Number
H2020 Marie Curie Actions of the European Commission	Germany	675555

Revision History  

• Version 1.0: 2020-12-09
  Type: Initial release
  
• Version 1.1: 2020-12-30
  Changes: Database references
• Version 1.2: 2024-01-24
  Changes: Data collection, Database references, Refinement description