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), 0.272 (DCC)
R-Value Work:
0.235 (Depositor)
R-Value Observed:
0.237 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history.

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.

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

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P38505
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SR Query on SR Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth B] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth B] MOL2 format, chain F [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth B] mmCIF format, chain F [auth B]	C [auth A], D [auth A], E [auth B], F [auth B]	STRONTIUM ION Sr PWYYWQHXAPXYMF-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.281 (Depositor), 0.272 (DCC)
R-Value Work: 0.235 (Depositor)
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

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Entry History

Deposition Data

Released Date: 2012-01-25

Deposition Author(s):

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.