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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.191 (Depositor), 0.192 (DCC)
R-Value Work:
0.189 (Depositor)
R-Value Observed:
0.189 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8UZ7

This is version 1.0 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A3R7QX74
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain G [auth C] SDF format, chain J [auth D] SDF format, chain K [auth D] SDF format, chain H [auth C] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain G [auth C] MOL2 format, chain J [auth D] MOL2 format, chain K [auth D] MOL2 format, chain H [auth C] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain G [auth C] mmCIF format, chain J [auth D] mmCIF format, chain K [auth D] mmCIF format, chain H [auth C] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A] F [auth A] G [auth C] H [auth C] J [auth D] E [auth A], F [auth A], G [auth C], H [auth C], J [auth D], K [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth C] Focus chain H [auth C] Focus chain J [auth D] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth C] Focus chain H [auth C] Focus chain J [auth D] Focus chain K [auth D]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain I [auth C] MOL2 format, chain I [auth C] mmCIF format, chain I [auth C]	I [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain I [auth C] Interactions & Density Focus chain I [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.191 (Depositor), 0.192 (DCC)
R-Value Work: 0.189 (Depositor)
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

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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.

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

Revision History (Full details and data files)

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

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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.