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), 0.258 (DCC)
R-Value Work:
0.212 (Depositor), 0.215 (DCC)
R-Value Observed:
0.214 (Depositor)

Starting Model: experimental
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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:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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), 0.258 (DCC)
R-Value Work: 0.212 (Depositor), 0.215 (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

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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

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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.