8WOH | pdb_00008woh

human dsDNA sensor CCDC25 complexed with 18bp DNA

PDB DOI: https://doi.org/10.2210/pdb8WOH/pdb
NAKB: 8WOH

Classification: DNA BINDING PROTEIN
Organism(s): synthetic construct, Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-10-07 Released: 2024-10-09
Deposition Author(s): Wen, Y., Wu, B.X.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free:
0.291 (Depositor), 0.292 (DCC)
R-Value Work:
0.230 (Depositor), 0.230 (DCC)
R-Value Observed:
0.233 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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

Literature

human dsDNA sensor CCDC25 complexed with 18bp DNA

Wen, Y., Wu, B.X.

To be published.

Macromolecule Content

Total Structure Weight: 57.59 kDa
Atom Count: 3,686
Modeled Residue Count: 400
Deposited Residue Count: 426
Unique protein chains: 1
Unique nucleic acid chains: 2

Macromolecules

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Coiled-coil domain-containing protein 25	C [auth B], D [auth A]	194	Homo sapiens	Mutation(s): 0 Gene Names: CCDC25
UniProt & NIH Common Fund Data Resources
Find proteins for Q86WR0 (Homo sapiens) Explore Q86WR0 Go to UniProtKB: Q86WR0
PHAROS: Q86WR0 GTEx: ENSG00000147419
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q86WR0
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism	Image
Entity ID: 1
18bp DNA	A [auth C]	19	synthetic construct
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism	Image
Entity ID: 2
18bp DNA	B [auth D]	19	synthetic construct
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free: 0.291 (Depositor), 0.292 (DCC)
R-Value Work: 0.230 (Depositor), 0.230 (DCC)
R-Value Observed: 0.233 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.66	α = 90
b = 77.964	β = 90
c = 99.378	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
autoPROC	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-10-09

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2024-10-09
Type: Initial release

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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.