3PX1 | pdb_00003px1

Structure of Calcium Binding Protein-1 from Entamoeba histolytica in complex with Strontium

• PDB DOI: https://doi.org/10.2210/pdb3PX1/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Entamoeba histolytica HM-1:IMSS
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-12-09 Released: 2012-01-25 
• Deposition Author(s): Kumar, S., Kumar, S., Ahmad, E., Khan, R.H., Gourinath, S.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.281 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.235 (Depositor), 0.270 (DCC) 
• R-Value Observed: 
  0.237 (Depositor) 

Starting Model: experimental

Literature

Flexibility and plasticity of EF-hand motifs: Structure of Calcium Binding Protein-1 from Entamoeba histolytica in complex with Pb2+, Ba2+, and Sr2+.

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

To be published.

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: 30.29 kDa 
• Atom Count: 1,027 
• Modeled Residue Count: 127 
• 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 HM-1:IMSS	Mutation(s): 0
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
SR	C [auth A], D [auth A], E [auth B], F [auth B]	STRONTIUM ION Sr PWYYWQHXAPXYMF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.281 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.235 (Depositor), 0.270 (DCC) 
• R-Value Observed: 0.237 (Depositor) 

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.429	α = 90
b = 95.429	β = 90
c = 63.973	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-01-25 
Deposition Author(s): Kumar, S., Kumar, S., Ahmad, E., Khan, R.H., Gourinath, S.

Revision History  

• Version 1.0: 2012-01-25
  Type: Initial release
  
• Version 1.1: 2017-11-08
  Changes: Refinement description
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description