5UPR

X-ray structure of a putative triosephosphate isomerase from Toxoplasma gondii ME49

PDB DOI: https://doi.org/10.2210/pdb5UPR/pdb

Classification: ISOMERASE
Organism(s): Toxoplasma gondii ME49
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2017-02-03 Released: 2017-02-22
Deposition Author(s): Filippova, E.V., Wawrzak, Z., Minasov, G., Cardona-Correa, A., Bishop, B., Anderson, W.F., Ngo, H., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.208
R-Value Work: 0.166
R-Value Observed: 0.168

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

X-ray structure of a putative triosephosphate isomerase from Toxoplasma gondii ME49

Filippova, E.V., Wawrzak, Z., Minasov, G., Cardona-Correa, A., Bishop, B., Anderson, W.F., Ngo, H., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 114.22 kDa
Atom Count: 8,876
Modelled Residue Count: 1,033
Deposited Residue Count: 1,060
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Triosephosphate isomerase	A, B, C, D	265	Toxoplasma gondii ME49	Mutation(s): 0 Gene Names: TPI-II, TGME49_233500 EC: 5.3.1.1
UniProt
Find proteins for A0A125YP67 (Toxoplasma gondii (strain ATCC 50611 / Me49)) Explore A0A125YP67 Go to UniProtKB: A0A125YP67
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A125YP67
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain E [auth A] 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 E [auth A] 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 E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain J [auth C] mmCIF format, chain L [auth D]	E [auth A], F [auth A], H [auth B], J [auth C], L [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain I [auth B] SDF format, chain K [auth C] SDF format, chain M [auth D] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] MOL2 format, chain K [auth C] MOL2 format, chain M [auth D] mmCIF format, chain G [auth A] mmCIF format, chain I [auth B] mmCIF format, chain K [auth C] mmCIF format, chain M [auth D]	G [auth A], I [auth B], K [auth C], M [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth D] Interactions & Density Focus chain G [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth D]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.208
R-Value Work: 0.166
R-Value Observed: 0.168
Space Group: P 1 2₁ 1
Diffraction Data: https://doi.org/10.18430/m35upr

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.368	α = 90
b = 115.533	β = 90.02
c = 78.719	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
PHENIX	phasing
Coot	model building

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2017-02-22

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2017-02-22
Type: Initial release
Version 1.1: 2017-07-19
Changes: Database references, Structure summary
Version 1.2: 2017-11-22
Changes: Refinement description
Version 1.3: 2024-11-20
Changes: Data collection, Database references, Refinement description, Structure summary