6VYE | pdb_00006vye

6-phosphogluconolactonase from Trypanosoma cruzi

PDB DOI: https://doi.org/10.2210/pdb6VYE/pdb

Classification: HYDROLASE
Organism(s): Trypanosoma cruzi strain CL Brener
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2020-02-26 Released: 2020-03-18
Deposition Author(s): Merritt, E.A., Structural Genomics of Pathogenic Protozoa Consortium (SGPP)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.270 (Depositor), 0.281 (DCC)
R-Value Work:
0.231 (Depositor), 0.244 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6VYE

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

Literature

6-phosphogluconolactonase from Trypanosoma cruzi

Merritt, E.A., Structural Genomics of Pathogenic Protozoa Consortium (SGPP), Hol, W.G.J., Buckner, F.S., Van Voorhis, W.C., Neely, H., Le Trong, I., Caruthers, J., Fan, E., Verlinde, C.L.M.J.

To be published.

Macromolecule Content

Total Structure Weight: 59.97 kDa
Atom Count: 4,317
Modeled Residue Count: 530
Deposited Residue Count: 542
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
6-phosphogluconolactonase	A, B	271	Trypanosoma cruzi strain CL Brener	Mutation(s): 0 Gene Names: Tc00.1047053503945.40 EC: 3.1.1.31
UniProt
Find proteins for Q4CQA8 (Trypanosoma cruzi (strain CL Brener)) Explore Q4CQA8 Go to UniProtKB: Q4CQA8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q4CQA8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain G [auth B] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain G [auth B] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], G [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain G [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A], F [auth A], H [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.270 (Depositor), 0.281 (DCC)
R-Value Work: 0.231 (Depositor), 0.244 (DCC)

Space Group: P 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.77	α = 90
b = 63.39	β = 94.91
c = 79.32	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MoRDa	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2020-03-18

Deposition Author(s):

Structural Genomics of Pathogenic Protozoa Consortium (SGPP)

Revision History (Full details and data files)

Version 1.0: 2020-03-18
Type: Initial release
Version 1.1: 2023-10-11
Changes: Data collection, Database references, 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.