4LRV | pdb_00004lrv

Crystal structure of DndE from Escherichia coli B7A involved in DNA phosphorothioation modification

• PDB DOI: https://doi.org/10.2210/pdb4LRV/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Escherichia coli B7A
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-07-21 Released: 2013-08-28 
• Deposition Author(s): Hu, W., Wang, C.K., Liang, J.D., Zhang, T.L., Yang, M., Hu, Z.P., Wang, Z.J., Lan, W.X., Wu, H.M., Ding, J.P., Wu, G., Deng, Z.X., Cao, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.242 (Depositor), 0.237 (DCC) 
• R-Value Work: 
  0.201 (Depositor), 0.198 (DCC) 
• R-Value Observed: 
  0.203 (Depositor) 

Literature

Structural insights into DndE from Escherichia coli B7A involved in DNA phosphorothioation modification

Hu, W., Wang, C.K., Liang, J.D., Zhang, T.L., Hu, Z.P., Wang, Z.J., Lan, W.X., Li, F., Wu, H.M., Ding, J.P., Wu, G., Deng, Z.X., Cao, C.

(2012) Cell Res 22: 1203-1206

• PubMed: 22525332 
• DOI: https://doi.org/10.1038/cr.2012.66
• Primary Citation Related Structures: 
  4LRV

Biological Assembly 1  

Global Symmetry: Dihedral - D4  (Explore in 3D)
Global Stoichiometry: Homo 8-mer - A8 

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

Biological Assembly 2  

Global Symmetry: Dihedral - D4  (Explore in 3D)
Global Stoichiometry: Homo 8-mer - A8 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Dihedral - D4  (Explore in 3D)
Global Stoichiometry: Homo 8-mer - A8 

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 201.19 kDa 
• Atom Count: 13,759 
• Modeled Residue Count: 1,675 
• Deposited Residue Count: 1,744 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA sulfur modification protein DndE	A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	109	Escherichia coli B7A	Mutation(s): 0  Gene Names: dndE, EcB7A_5348

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.242 (Depositor), 0.237 (DCC) 
• R-Value Work:  0.201 (Depositor), 0.198 (DCC) 
• R-Value Observed: 0.203 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.845	α = 90
b = 97.306	β = 95.81
c = 218.532	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHENIX	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-08-28 
Deposition Author(s): Hu, W., Wang, C.K., Liang, J.D., Zhang, T.L., Yang, M., Hu, Z.P., Wang, Z.J., Lan, W.X., Wu, H.M., Ding, J.P., Wu, G., Deng, Z.X., Cao, C.

Revision History  

• Version 1.0: 2013-08-28
  Type: Initial release
  
• Version 1.1: 2013-09-04
  Changes: Experimental preparation
• Version 1.2: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary