6O93

D-alanyl transferase DltD from Enterococcus faecalis

• PDB DOI: https://doi.org/10.2210/pdb6O93/pdb

• Classification: TRANSFERASE
• Organism(s): Enterococcus faecalis V583
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-03-12 Released: 2019-03-27 
• Deposition Author(s): Shakhashiro, M., Korotkov, K.V.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.18 Å
• R-Value Free: 0.219 
• R-Value Work: 0.183 
• R-Value Observed: 0.185 

Literature

D-alanyl transferase DltD from Enterococcus faecalis

Shakhashiro, M., Williamson, Z.A., Korotkova, N., Korotkov, K.V.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 46.52 kDa 
• Atom Count: 3,502 
• Modelled Residue Count: 394 
• Deposited Residue Count: 398 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-alanyl transferase DltD	A	398	Enterococcus faecalis V583	Mutation(s): 0  Gene Names: dltD, EF_2746
UniProt
Find proteins for Q830N3 (Enterococcus faecalis (strain ATCC 700802 / V583)) Explore Q830N3  Go to UniProtKB:  Q830N3

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	E [auth A], F [auth A], G [auth A], H [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	B [auth A], C [auth A], D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	I [auth A], J [auth A], L [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	K [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.18 Å
• R-Value Free: 0.219 
• R-Value Work: 0.183 
• R-Value Observed: 0.185 
• Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.75	α = 90
b = 102.75	β = 90
c = 205.75	γ = 120

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-03-27 
Deposition Author(s): Shakhashiro, M., Korotkov, K.V.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P30GM110787

Revision History  

• Version 1.0: 2019-03-27
  Type: Initial release
  
• Version 1.1: 2020-01-01
  Changes: Author supporting evidence
• Version 1.2: 2023-10-11
  Changes: Data collection, Database references, Refinement description