8IW2 | pdb_00008iw2

Entamoeba histolytica Pyruvate kinase

PDB DOI: https://doi.org/10.2210/pdb8IW2/pdb

Classification: CYTOSOLIC PROTEIN
Organism(s): Entamoeba histolytica HM-1:IMSS
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-03-29 Released: 2024-04-10
Deposition Author(s): Rath, P.P., Gourinath, S., Kumari, P.
Funding Organization(s): Department of Science & Technology (DST, India)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free:
0.202 (Depositor), 0.200 (DCC)
R-Value Work:
0.171 (Depositor), 0.170 (DCC)

wwPDB Validation 3D Report Full Report

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

Literature

Entamoeba histolytica Pyruvate kinase

Rath, P.P., Gourinath, S.

To be published.

Macromolecule Content

Total Structure Weight: 36.92 kDa
Atom Count: 2,717
Modeled Residue Count: 321
Deposited Residue Count: 321
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pyruvate kinase	A	321	Entamoeba histolytica HM-1:IMSS	Mutation(s): 0 Gene Names: EHI_098420 EC: 2.7.1.40
UniProt
Find proteins for N9V1V2 (Entamoeba histolytica HM-1:IMSS-A) Explore N9V1V2 Go to UniProtKB: N9V1V2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	N9V1V2
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.202 (Depositor), 0.200 (DCC)
R-Value Work: 0.171 (Depositor), 0.170 (DCC)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.801	α = 90
b = 89.536	β = 90
c = 37.138	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
SHELXCD	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-04-10

Deposition Author(s):

Funding Organization	Location	Grant Number
Department of Science & Technology (DST, India)	India	CRG/2020/000177

Revision History (Full details and data files)

Version 1.0: 2024-04-10
Type: Initial release
Version 1.1: 2024-10-30
Changes: Structure summary

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.