6PFX | pdb_00006pfx

D-alanyl transferase DltD from Enterococcus faecium

• PDB DOI: https://doi.org/10.2210/pdb6PFX/pdb

• Classification: TRANSFERASE
• Organism(s): Enterococcus faecium TX0133a04
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-06-22 Released: 2019-07-03 
• Deposition Author(s): Shakhashiro, M., Korotkov, K.V.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.211 (Depositor), 0.212 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.189 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

Starting Model: experimental

Literature

D-alanyl transferase DltD from Enterococcus faecium

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 and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

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

Macromolecule Content 

• Total Structure Weight: 92.97 kDa 
• Atom Count: 6,989 
• Modeled Residue Count: 766 
• Deposited Residue Count: 794 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-alanyl transferase DltD	A, B	397	Enterococcus faecium TX0133a04	Mutation(s): 0  Gene Names:  dltD, AWT83_05715, B4W81_00525, BU187_05285, BU190_00460, BU192_07235, BXT96_01745, CQR37_04475, CUM68_11350, CUS36_06310, DKP91_06765, DTPHA_600407, EB12_02182, NCTC13923_01752
UniProt
Find proteins for Q3XZT4 (Enterococcus faecium (strain ATCC BAA-472 / TX0016 / DO)) Explore Q3XZT4  Go to UniProtKB:  Q3XZT4

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A], D [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.211 (Depositor), 0.212 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.189 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.255	α = 90
b = 76.434	β = 117.725
c = 78.4	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-07-03 
Deposition Author(s): Shakhashiro, M., Korotkov, K.V.

---

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: 2019-07-03
  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