4E2B | pdb_00004e2b

High resolution crystal structure of the old yellow enzyme from Trypanosoma cruzi

• PDB DOI: https://doi.org/10.2210/pdb4E2B/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: 1.27 Å
• R-Value Free: 
  0.171 (Depositor), 0.153 (DCC) 
• R-Value Work: 
  0.146 (Depositor), 0.131 (DCC) 
• R-Value Observed: 
  0.147 (Depositor) 

Starting Model: experimental

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)

Macromolecule Content 

• Total Structure Weight: 43.61 kDa 
• Atom Count: 3,470 
• Modeled Residue Count: 378 
• Deposited Residue Count: 382 
• Unique protein chains: 1

Macromolecules

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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMN	B [auth A]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N
PEG	E [auth A], F [auth A], G [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL	C [auth A], D [auth A], H [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.27 Å
• R-Value Free:  0.171 (Depositor), 0.153 (DCC) 
• R-Value Work:  0.146 (Depositor), 0.131 (DCC) 
• R-Value Observed: 0.147 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.347	α = 90
b = 68.656	β = 90
c = 85.19	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