3QTP | pdb_00003qtp

Crystal Structure Analysis of Entamoeba histolytica Enolase

PDB DOI: https://doi.org/10.2210/pdb3QTP/pdb

Classification: LYASE
Organism(s): Entamoeba histolytica
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2011-02-23 Released: 2011-07-13
Deposition Author(s): Schulz, E.C., Ficner, R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.202 (Depositor), 0.200 (DCC)
R-Value Work:
0.153 (Depositor), 0.154 (DCC)
R-Value Observed:
0.155 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structure analysis of Entamoeba histolytica enolase.

Schulz, E.C., Tietzel, M., Tovy, A., Ankri, S., Ficner, R.

(2011) Acta Crystallogr D Biol Crystallogr 67: 619-627

PubMed: 21697600 Search on PubMed
DOI: https://doi.org/10.1107/S0907444911016544
Primary Citation Related Structures:
3QTP

PubMed Abstract:
Entamoeba histolytica enolase (EhENO) reversibly interconverts 2-phosphoglyceric acid (2-PGA) and phosphoenolpyruvic acid (PEP). The crystal structure of the homodimeric EhENO is presented at a resolution of 1.9 Å. In the crystal structure EhENO presents as an asymmetric dimer with one active site in the open conformation and the other active site in the closed conformation. Interestingly, both active sites contain a copurified 2-PGA molecule. While the 2-PGA molecule in the closed active site closely resembles the conformation known from other enolase-2-PGA complexes, the conformation in the open active site is different. Here, 2-PGA is shifted approximately 1.6 Å away from metal ion I, most likely representing a precatalytic situation.

Organizational Affiliation

Abteilung für Molekulare Strukturbiologie, Institut für Mikrobiologie und Genetik, Georg-August-Universität Göttingen, Justus-von-Liebig Weg, Germany. eschulz1@gwdg.de

Macromolecule Content

Total Structure Weight: 96.59 kDa
Atom Count: 7,941
Modeled Residue Count: 877
Deposited Residue Count: 882
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Enolase 1	A, B	441	Entamoeba histolytica	Mutation(s): 0 Gene Names: ENL-1 EC: 4.2.1.11
UniProt
Find proteins for P51555 (Entamoeba histolytica (strain ATCC 30459 / HM-1:IMSS / ABRM)) Explore P51555 Go to UniProtKB: P51555
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P51555
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
2PG Query on 2PG Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain H [auth B] MOL2 format, chain C [auth A] MOL2 format, chain H [auth B] mmCIF format, chain C [auth A] mmCIF format, chain H [auth B]	C [auth A], H [auth B]	2-PHOSPHOGLYCERIC ACID C₃ H₇ O₇ P GXIURPTVHJPJLF-UWTATZPHSA-N		Interactions Focus chain C [auth A] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain H [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B]	D [auth A] E [auth A] F [auth A] I [auth B] J [auth B] D [auth A], E [auth A], F [auth A], I [auth B], J [auth B], K [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain L [auth B] MOL2 format, chain G [auth A] MOL2 format, chain L [auth B] mmCIF format, chain G [auth A] mmCIF format, chain L [auth B]	G [auth A], L [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain L [auth B] Interactions & Density Focus chain G [auth A] Focus chain L [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.202 (Depositor), 0.200 (DCC)
R-Value Work: 0.153 (Depositor), 0.154 (DCC)
R-Value Observed: 0.155 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.42	α = 90
b = 92.62	β = 90
c = 160.58	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
DNA	data collection
XDS	data reduction
PHENIX	refinement

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2011-07-13

Deposition Author(s):

Schulz, E.C.

Ficner, R.

Revision History (Full details and data files)

Version 1.0: 2011-07-13
Type: Initial release
Version 1.1: 2024-10-30
Changes: Data collection, Database references, Derived calculations, Structure summary