5WTU

Crystal structure of DndE G21/24K mutant involved in DNA phosphorothioation

PDB DOI: https://doi.org/10.2210/pdb5WTU/pdb

Classification: DNA BINDING PROTEIN
Organism(s): Escherichia coli
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2016-12-14 Released: 2018-02-21
Deposition Author(s): Yao, P., Liu, Y., Wang, C., Cao, C.
Funding Organization(s): National Natural Science Foundation of China

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.272
R-Value Work: 0.225
R-Value Observed: 0.227

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of DndE G21/24K mutant involved in DNA phosphorothioation

Yao, P., Liu, Y., Wang, C., Cao, C.

To be published.

Macromolecule Content

Total Structure Weight: 50.76 kDa
Atom Count: 3,114
Modelled Residue Count: 388
Deposited Residue Count: 440
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA sulfur modification protein DndE	A, B, C, D	110	Escherichia coli	Mutation(s): 2 Gene Names: ACU90_25985
UniProt
Find proteins for A0A0N8J336 (Escherichia coli) Explore A0A0N8J336 Go to UniProtKB: A0A0N8J336
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0N8J336
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.272
R-Value Work: 0.225
R-Value Observed: 0.227
Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.297	α = 90
b = 57.297	β = 90
c = 130.222	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2018-02-21

Deposition Author(s):

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

Revision History (Full details and data files)

Version 1.0: 2018-02-21
Type: Initial release
Version 1.1: 2024-03-20
Changes: Data collection, Database references

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.