5F3Q

Crystal structure of a noncanonical Dicer protein from Entamoeba histolytica

PDB DOI: https://doi.org/10.2210/pdb5F3Q/pdb

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

Deposited: 2015-12-03 Released: 2016-12-14
Deposition Author(s): Yu, X., Gan, J.H., Ma, J.B.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.246
R-Value Work: 0.202
R-Value Observed: 0.204

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Structural and functional study of a noncanonical Dicer protein in Entamoeba histolytica

Yu, X., Gan, J.H., Ma, J.B.

To be published.

Macromolecule Content

Total Structure Weight: 45.75 kDa
Atom Count: 3,065
Modelled Residue Count: 360
Deposited Residue Count: 386
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative uncharacterized protein	A, B	193	Entamoeba histolytica	Mutation(s): 0 Gene Names: EHI_068740
UniProt
Find proteins for C4LU64 (Entamoeba histolytica (strain ATCC 30459 / HM-1:IMSS / ABRM)) Explore C4LU64 Go to UniProtKB: C4LU64
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	C4LU64
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B]	C [auth A], D [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.246
R-Value Work: 0.202
R-Value Observed: 0.204
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.281	α = 90
b = 91.015	β = 90
c = 102.746	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data processing
Coot	model building
PHENIX	refinement

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2016-12-14

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-12-14
Type: Initial release

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.