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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.175 (Depositor), 0.161 (DCC) 
• R-Value Work: 
  0.146 (Depositor) 
• R-Value Observed: 
  0.147 (Depositor) 

Literature

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

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

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 and generated by PISA (software)

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

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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	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
EDO	K [auth B], O [auth C], P [auth C]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
NA	E [auth A], H [auth B], L [auth C], Q [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.175 (Depositor), 0.161 (DCC) 
• R-Value Work:  0.146 (Depositor) 
• 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

Entry History 

Deposition Data

• Released Date: 2010-07-21 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• 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