8DPE | pdb_00008dpe

Crystal structure of ATP-dependent RNA helicase DDX42

PDB DOI: https://doi.org/10.2210/pdb8DPE/pdb

Classification: SPLICING, HYDROLASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-07-15 Released: 2022-08-24
Deposition Author(s): Larsen, N.A., Tsai, J.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.53 Å
R-Value Free:
0.255 (Depositor), 0.260 (DCC)
R-Value Work:
0.212 (Depositor), 0.210 (DCC)
R-Value Observed:
0.214 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of ATP-dependent RNA helicase DDX42

Larsen, N.A.

To be published.

Macromolecule Content

Total Structure Weight: 49.87 kDa
Atom Count: 3,802
Modeled Residue Count: 436
Deposited Residue Count: 444
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-dependent RNA helicase DDX42	A	444	Homo sapiens	Mutation(s): 0 Gene Names: DDX42 EC: 3.6.4.13
UniProt & NIH Common Fund Data Resources
Find proteins for Q86XP3 (Homo sapiens) Explore Q86XP3 Go to UniProtKB: Q86XP3
PHAROS: Q86XP3 GTEx: ENSG00000198231
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q86XP3
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.53 Å
R-Value Free: 0.255 (Depositor), 0.260 (DCC)
R-Value Work: 0.212 (Depositor), 0.210 (DCC)
R-Value Observed: 0.214 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.917	α = 90
b = 73.268	β = 90
c = 134.041	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
MOLREP	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2022-08-24

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded	United States	--

Revision History (Full details and data files)

Version 1.0: 2022-08-24
Type: Initial release
Version 1.1: 2023-10-18
Changes: Data collection, Refinement description

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.