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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 
  0.272 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.225 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.227 (Depositor) 

Literature

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

Yao, P., Liu, Y., Wang, C., Cao, C.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

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

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.272 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.225 (Depositor), 0.210 (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

Entry History & Funding Information

Deposition Data

• Released Date: 2018-02-21 
Deposition Author(s): Yao, P., Liu, Y., Wang, C., Cao, C.

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

Revision History  

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