7YMF | pdb_00007ymf

Crystal Structure of DDX3X449_450ET>DP

PDB DOI: https://doi.org/10.2210/pdb7YMF/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2022-07-28 Released: 2024-01-03
Deposition Author(s): Xiong, J.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.244 (Depositor), 0.243 (DCC)
R-Value Work:
0.185 (Depositor), 0.186 (DCC)
R-Value Observed:
0.188 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 7YMF

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

Literature

Crystal Structure of DDX3X449_450ET>DP

Xiong, J.

To be published.

Macromolecule Content

Total Structure Weight: 54.44 kDa
Atom Count: 3,523
Modeled Residue Count: 417
Deposited Residue Count: 481
Unique protein chains: 2

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-dependent RNA helicase DDX3X	A	303	Homo sapiens	Mutation(s): 0 Gene Names: DDX3X EC: 3.6.4.13
UniProt & NIH Common Fund Data Resources
Find proteins for O00571 (Homo sapiens) Explore O00571 Go to UniProtKB: O00571
PHAROS: O00571 GTEx: ENSG00000215301
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O00571
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-dependent RNA helicase DDX3X	B	178	Homo sapiens	Mutation(s): 2 Gene Names: DDX3X EC: 3.6.4.13
UniProt & NIH Common Fund Data Resources
Find proteins for O00571 (Homo sapiens) Explore O00571 Go to UniProtKB: O00571
PHAROS: O00571 GTEx: ENSG00000215301
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O00571
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.244 (Depositor), 0.243 (DCC)
R-Value Work: 0.185 (Depositor), 0.186 (DCC)
R-Value Observed: 0.188 (Depositor)

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.56	α = 90
b = 106.56	β = 90
c = 116.71	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2024-01-03

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History (Full details and data files)

Version 1.0: 2024-01-03
Type: Initial release
Version 1.1: 2026-03-04
Changes: Refinement description, Structure summary

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.