5F3Q | pdb_00005f3q

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 (Depositor), 0.260 (DCC)
R-Value Work:
0.202 (Depositor)
R-Value Observed:
0.204 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 5F3Q

This is version 1.1 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
Modeled Residue Count: 360
Deposited Residue Count: 386
Unique protein chains: 1

Macromolecules

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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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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 D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	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 (Depositor), 0.260 (DCC)
R-Value Work: 0.202 (Depositor)
R-Value Observed: 0.204 (Depositor)

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

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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
Version 1.1: 2024-11-20
Changes: Data collection, Database references, Structure summary

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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.