7DXM

Crystal structure of DltD

• PDB DOI: https://doi.org/10.2210/pdb7DXM/pdb

• Classification: TRANSFERASE
• Organism(s): Streptococcus thermophilus LMG 18311
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2021-01-19 Released: 2021-07-21 
• Deposition Author(s): Yan, X.X., Zeng, Q., Tian, L.F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.96 Å
• R-Value Free: 0.228 
• R-Value Work: 0.216 

Literature

Crystal Structure of an O-acyltransfer Terminal Protein stDltD and Its Implications for dlt Operon-mediated D-alanylation of S. thermophilus.

Zeng, Q., Tian, L.F., Liu, Y.P., Yan, X.X., Xu, W.Q.

(2022) PROG BIOCHEM BIOPHYS 48: 1052-1062

• DOI: https://doi.org/10.16476/j.pibb.2021.0020

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Macromolecule Content

• Total Structure Weight: 183.7 kDa 
• Atom Count: 12,785 
• Modelled Residue Count: 1,564 
• Deposited Residue Count: 1,588 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein DltD	A, B, C, D	397	Streptococcus thermophilus LMG 18311	Mutation(s): 0  Gene Names: dltD
UniProt
Find proteins for Q5M4V2 (Streptococcus thermophilus (strain ATCC BAA-250 / LMG 18311)) Explore Q5M4V2  Go to UniProtKB:  Q5M4V2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4 (Subject of Investigation/LOI)	E [auth A], F [auth A], G [auth B], H [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.96 Å
• R-Value Free: 0.228 
• R-Value Work: 0.216 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.273	α = 90
b = 109.92	β = 90
c = 282.377	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-07-21 
Deposition Author(s): Yan, X.X., Zeng, Q., Tian, L.F.

Revision History  

• Version 1.0: 2021-07-21
  Type: Initial release
  
• Version 1.1: 2022-08-03
  Changes: Database references, Structure summary
• Version 1.2: 2023-11-29
  Changes: Data collection, Refinement description