4E2D

Structure of the old yellow enzyme from Trypanosoma cruzi

• PDB DOI: https://doi.org/10.2210/pdb4E2D/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Trypanosoma cruzi
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-03-08 Released: 2013-03-27 
• Deposition Author(s): Murakami, M.T., Rodrigues, N.C., Gava, L.M., Canduri, F., Oliva, G., Barbosa, L.R.S., Borgers, J.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.242 
• R-Value Work: 0.194 
• R-Value Observed: 0.196 

Literature

High resolution crystal structure and in solution studies of the Old Yellow Enzyme from Trypanosoma cruzi: Insights into oligomerization, enzyme dynamics and specificity

Murakami, M.T., Rodrigues, N.C., Gava, L.M., Canduri, F., Oliva, G., Barbosa, L.R.S., Borgers, J.C.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 172.37 kDa 
• Atom Count: 12,421 
• Modelled Residue Count: 1,507 
• Deposited Residue Count: 1,528 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Old Yellow Protein	A, B, C, D	382	Trypanosoma cruzi	Mutation(s): 0
UniProt
Find proteins for Q2TJB8 (Trypanosoma cruzi) Explore Q2TJB8  Go to UniProtKB:  Q2TJB8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMN	E [auth A], G [auth B], I [auth C], K [auth D]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N
DMS	F [auth A], H [auth B], J [auth C], L [auth D]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.242 
• R-Value Work: 0.194 
• R-Value Observed: 0.196 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.774	α = 90
b = 118.469	β = 90.09
c = 111.123	γ = 90

Software Package:

Software Name	Purpose
NatXray	data collection
MOLREP	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-03-27 
Deposition Author(s): Murakami, M.T., Rodrigues, N.C., Gava, L.M., Canduri, F., Oliva, G., Barbosa, L.R.S., Borgers, J.C.

Revision History  

• Version 1.0: 2013-03-27
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description