9K3E | pdb_00009k3e

DddB(BadTF3) dsDNA deaminase

PDB DOI: https://doi.org/10.2210/pdb9K3E/pdb

Classification: HYDROLASE
Organism(s): Taylorella equigenitalis MCE9
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-10-18 Released: 2024-11-27
Deposition Author(s): Dong, W.Y., Xiaoliang, S.X.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.240 (Depositor), 0.241 (DCC)
R-Value Work:
0.194 (Depositor), 0.197 (DCC)
R-Value Observed:
0.199 (Depositor)

Starting Model: in silico
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Genome-wide mapping of human transcription factors' footprints with double-stranded DNA deaminase

Wenyang, D., Xiaoliang, S.X.

To be published.

Macromolecule Content

Total Structure Weight: 28.73 kDa
Atom Count: 1,862
Modeled Residue Count: 224
Deposited Residue Count: 252
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
YD repeat protein	A [auth B]	135	Taylorella equigenitalis MCE9	Mutation(s): 0 Gene Names: TEQUI_0434
UniProt
Find proteins for A0A654KG07 (Taylorella equigenitalis (strain MCE9)) Explore A0A654KG07 Go to UniProtKB: A0A654KG07
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A654KG07
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
The immunity protein of DddB	B [auth C]	117	Taylorella equigenitalis MCE9	Mutation(s): 0 Gene Names: TEQUI_0433
UniProt
Find proteins for A0A654KG21 (Taylorella equigenitalis (strain MCE9)) Explore A0A654KG21 Go to UniProtKB: A0A654KG21
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A654KG21
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.240 (Depositor), 0.241 (DCC)
R-Value Work: 0.194 (Depositor), 0.197 (DCC)
R-Value Observed: 0.199 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.069	α = 90
b = 130.646	β = 90
c = 61.618	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	phasing
CrysalisPro	data reduction
CrysalisPro	data scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-11-27

Deposition Author(s):

Xiaoliang, S.X.

Funding Organization	Location	Grant Number
Other government		--

Revision History (Full details and data files)

Version 1.0: 2024-11-27
Type: Initial release

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.