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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.242 (Depositor), 0.260 (DCC)
R-Value Work:
0.194 (Depositor), 0.210 (DCC)
R-Value Observed:
0.196 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

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.

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

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2TJB8
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FMN Query on FMN Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain I [auth C] SDF format, chain K [auth D] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain I [auth C] MOL2 format, chain K [auth D] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain I [auth C] mmCIF format, chain K [auth D]	E [auth A], G [auth B], I [auth C], K [auth D]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D]
DMS Query on DMS Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain J [auth C] SDF format, chain L [auth D] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain J [auth C] MOL2 format, chain L [auth D] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain J [auth C] mmCIF format, chain L [auth D]	F [auth A], H [auth B], J [auth C], L [auth D]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.242 (Depositor), 0.260 (DCC)
R-Value Work: 0.194 (Depositor), 0.210 (DCC)
R-Value Observed: 0.196 (Depositor)

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

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2013-03-27

Deposition Author(s):

Revision History (Full details and data files)

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