8UZ7 | pdb_00008uz7

Crystal structure of a novel triose phosphate isomerase identified on the shrimp transcriptome

• PDB DOI: https://doi.org/10.2210/pdb8UZ7/pdb

• Classification: ISOMERASE
• Organism(s): Penaeus vannamei
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-11-14 Released: 2023-12-06 
• Deposition Author(s): Sotelo-Mundo, R.R., Gomez-Yanes, A.C., Lopez-Zavala, A.A., Lopez-Garcia, J.A., Ochoa-Leyva, A.
• Funding Organization(s): Consejo Nacional de Ciencia y Tecnologia (CONACYT), Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.191 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.189 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.189 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a novel triose phosphate isomerase from shrimp

Sotelo-Mundo, R.R., Gomez-Yanes, A.C., Lopez-Zavala, A.A., Ochoa-Leyva, A.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 110 kDa 
• Atom Count: 8,125 
• Modeled Residue Count: 976 
• Deposited Residue Count: 996 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Triosephosphate isomerase	A, B, C, D	249	Penaeus vannamei	Mutation(s): 0  Gene Names: C7M84_025338 EC: 5.3.1.1
UniProt
Find proteins for A0A3R7QX74 (Penaeus vannamei) Explore A0A3R7QX74  Go to UniProtKB:  A0A3R7QX74

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	E [auth A], F [auth A], G [auth C], H [auth C], J [auth D], K [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	I [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.191 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.189 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.189 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.564	α = 90
b = 84.253	β = 92.69
c = 73.739	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-12-06 
Deposition Author(s): Sotelo-Mundo, R.R., Gomez-Yanes, A.C., Lopez-Zavala, A.A., Lopez-Garcia, J.A., Ochoa-Leyva, A.

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Funding Organization	Location	Grant Number
Consejo Nacional de Ciencia y Tecnologia (CONACYT)	Mexico	CF-2019-263986
Not funded		UNAM PAPIIT IN215520

Revision History  

• Version 1.0: 2023-12-06
  Type: Initial release