5WTU | pdb_00005wtu

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 (Depositor), 0.238 (DCC)
R-Value Work:
0.225 (Depositor), 0.209 (DCC)
R-Value Observed:
0.227 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 5WTU

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
Modeled Residue Count: 388
Deposited Residue Count: 440
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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 (Depositor), 0.238 (DCC)
R-Value Work: 0.225 (Depositor), 0.209 (DCC)
R-Value Observed: 0.227 (Depositor)

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

View more in-depth experimental data

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 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.