3ULG

Crystal structure of Calcium-Binding Protein-1 from Entamoeba histolytica in complex with barium

• PDB DOI: https://doi.org/10.2210/pdb3ULG/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Entamoeba histolytica
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-11-10 Released: 2012-10-24 
• Deposition Author(s): Kumar, S., Gourinath, S.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 0.314 
• R-Value Work: 0.247 
• R-Value Observed: 0.250 

Literature

Flexibility of EF-hand motifs: Structural and thermodynamic studies of Calcium Binding Protein- 1 from Entamoeba histolytica with Pb2+, Ba2+, and Sr2+

Kumar, S., Ahmed, E., Kumar, S., Khan, R.H., Gourinath, S.

(2012) BMC Biophys 5: 15-15

• PubMed: 22906057 
• DOI: https://doi.org/10.1186/2046-1682-5-15
• Primary Citation of Related Structures:  
  3ULG


• PubMed Abstract: 
  

  EF-hand proteins can be activated by the binding of various heavy metals other than calcium, and such complexes can disturb the calcium-signaling pathway and cause toxicity and disease causing state. So far, no comprehensive study has been done to understand different heavy metals binding to calcium signaling proteins.

---

Organizational Affiliation: 

School of Life Sciences, Jawaharlal Nehru University, New Delhi, India. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 30.77 kDa 
• Atom Count: 993 
• Modelled Residue Count: 124 
• Deposited Residue Count: 268 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Calcium-binding protein	A, B	134	Entamoeba histolytica	Mutation(s): 0  Gene Names: CaBP1
UniProt
Find proteins for P38505 (Entamoeba histolytica (strain ATCC 30459 / HM-1:IMSS / ABRM)) Explore P38505  Go to UniProtKB:  P38505

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BA	C [auth A], D [auth A], E [auth A], F [auth B], G [auth B], H [auth B]	BARIUM ION Ba XDFCIPNJCBUZJN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 0.314 
• R-Value Work: 0.247 
• R-Value Observed: 0.250 
• Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.21	α = 90
b = 95.21	β = 90
c = 62.986	γ = 120

Software Package:

Software Name	Purpose
MAR345dtb	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-10-24 
Deposition Author(s): Kumar, S., Gourinath, S.

Revision History  

• Version 1.0: 2012-10-24
  Type: Initial release
  
• Version 1.1: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description