3QJK | pdb_00003qjk

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

• PDB DOI: https://doi.org/10.2210/pdb3QJK/pdb

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


• Deposited: 2011-01-29 Released: 2012-04-11 
• Deposition Author(s): Kumar, S., Gourinath, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.283 (Depositor), 0.288 (DCC) 
• R-Value Work: 
  0.252 (Depositor), 0.256 (DCC) 
• R-Value Observed: 
  0.255 (Depositor) 

Starting Model: experimental

Literature

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

Kumar, S., 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: 30.89 kDa 
• Atom Count: 1,025 
• 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  Gene Names: EhCaBP1
UniProt
Find proteins for P38505 (Entamoeba histolytica (strain ATCC 30459 / HM-1:IMSS / ABRM)) Explore P38505  Go to UniProtKB:  P38505

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PB	C [auth A], D [auth A], F [auth B], G [auth B]	LEAD (II) ION Pb RVPVRDXYQKGNMQ-UHFFFAOYSA-N
ACT	E [auth A], H [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.283 (Depositor), 0.288 (DCC) 
• R-Value Work:  0.252 (Depositor), 0.256 (DCC) 
• R-Value Observed: 0.255 (Depositor) 

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.264	α = 90
b = 95.264	β = 90
c = 64.597	γ = 120

Software Package:

Software Name	Purpose
MAR345dtb	data collection
PHASER	phasing
CNS	refinement
AUTOMAR	data reduction
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-04-11 
Deposition Author(s): Kumar, S., Gourinath, S.

Revision History  

• Version 1.0: 2012-04-11
  Type: Initial release
  
• Version 1.1: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description