3QJK

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.283
R-Value Work: 0.252
R-Value Observed: 0.255

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

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

Kumar, S., Gourinath, S.

To be published.

Macromolecule Content

Total Structure Weight: 30.89 kDa
Atom Count: 1,025
Modelled Residue Count: 127
Deposited Residue Count: 268
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P38505
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PB Query on PB Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain F [auth B] SDF format, chain G [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth B]	C [auth A], D [auth A], F [auth B], G [auth B]	LEAD (II) ION Pb RVPVRDXYQKGNMQ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain F [auth B] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain F [auth B] Focus chain G [auth B]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B]	E [auth A], H [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain H [auth B] Interactions & Density Focus chain E [auth A] Focus chain H [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.283
R-Value Work: 0.252
R-Value Observed: 0.255
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

View Full Validation Report

Entry History

Deposition Data

Released Date: 2012-04-11

Deposition Author(s):

Kumar, S.

Gourinath, S.

Revision History (Full details and data files)

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

Prepare Data

Validate Data

Deposit Data

Help and Resources

3QJK

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

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

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)