3NGJ | pdb_00003ngj

Crystal structure of a putative deoxyribose-phosphate aldolase from Entamoeba histolytica

PDB DOI: https://doi.org/10.2210/pdb3NGJ/pdb

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

Deposited: 2010-06-11 Released: 2010-07-21
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.175 (Depositor), 0.181 (DCC)
R-Value Work:
0.146 (Depositor), 0.154 (DCC)
R-Value Observed:
0.147 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of a putative deoxyribose-phosphate aldolase from Entamoeba histolytica

Abendroth, J., Gardberg, A., Staker, B.

To be published.

Macromolecule Content

Total Structure Weight: 102.8 kDa
Atom Count: 7,564
Modeled Residue Count: 879
Deposited Residue Count: 956
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Deoxyribose-phosphate aldolase	A, B, C, D	239	Entamoeba histolytica	Mutation(s): 0 Gene Names: EHI_121800 EC: 4.1.2.4
UniProt
Find proteins for C4M5C6 (Entamoeba histolytica (strain ATCC 30459 / HM-1:IMSS / ABRM)) Explore C4M5C6 Go to UniProtKB: C4M5C6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	C4M5C6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain M [auth C] SDF format, chain N [auth C] SDF format, chain R [auth D] SDF format, chain S [auth D] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain M [auth C] MOL2 format, chain N [auth C] MOL2 format, chain R [auth D] MOL2 format, chain S [auth D] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain M [auth C] mmCIF format, chain N [auth C] mmCIF format, chain R [auth D] mmCIF format, chain S [auth D]	F [auth A] G [auth A] I [auth B] J [auth B] M [auth C] F [auth A], G [auth A], I [auth B], J [auth B], M [auth C], N [auth C], R [auth D], S [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain R [auth D] Focus chain S [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain R [auth D] Focus chain S [auth D]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain O [auth C] SDF format, chain P [auth C] MOL2 format, chain K [auth B] MOL2 format, chain O [auth C] MOL2 format, chain P [auth C] mmCIF format, chain K [auth B] mmCIF format, chain O [auth C] mmCIF format, chain P [auth C]	K [auth B], O [auth C], P [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain K [auth B] Focus chain O [auth C] Focus chain P [auth C] Interactions & Density Focus chain K [auth B] Focus chain O [auth C] Focus chain P [auth C]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain L [auth C] SDF format, chain Q [auth D] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain L [auth C] MOL2 format, chain Q [auth D] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain L [auth C] mmCIF format, chain Q [auth D]	E [auth A], H [auth B], L [auth C], Q [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain L [auth C] Focus chain Q [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain L [auth C] Focus chain Q [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.175 (Depositor), 0.181 (DCC)
R-Value Work: 0.146 (Depositor), 0.154 (DCC)
R-Value Observed: 0.147 (Depositor)

Diffraction Data: https://doi.org/10.18430/M33NGJ

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.26	α = 90
b = 70.78	β = 92.46
c = 126.75	γ = 90

Software Package:

Software Name	Purpose
BOS	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2010-07-21

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2010-07-21
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2024-11-27
Changes: Data collection, Database references, Derived calculations, Structure summary