6OSU | pdb_00006osu

Crystal Structure of the D-alanyl-D-alanine carboxypeptidase DacD from Francisella tularensis

• PDB DOI: https://doi.org/10.2210/pdb6OSU/pdb

• Classification: HYDROLASE
• Organism(s): Francisella tularensis subsp. tularensis SCHU S4
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-05-02 Released: 2019-05-15 
• Deposition Author(s): Kim, Y., Stogios, P., Skarina, T., Di, R., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.44 Å
• R-Value Free: 
  0.229 (Depositor), 0.234 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.188 (DCC) 
• R-Value Observed: 
  0.185 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of the D-alanyl-D-alanine carboxypeptidase DacD from Francisella tularensis

Kim, Y., Stogios, P., Skarina, T., Di, R., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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)

Macromolecule Content 

• Total Structure Weight: 46.5 kDa 
• Atom Count: 3,202 
• Modeled Residue Count: 413 
• Deposited Residue Count: 427 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-alanyl-D-alanine carboxypeptidase (Penicillin binding protein) family protein	A	427	Francisella tularensis subsp. tularensis SCHU S4	Mutation(s): 0  Gene Names: dacD, FTT_1029, BZ14_1819 EC: 3.4.16.4
UniProt
Find proteins for Q5NG28 (Francisella tularensis subsp. tularensis (strain SCHU S4 / Schu 4)) Explore Q5NG28  Go to UniProtKB:  Q5NG28

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.44 Å
• R-Value Free:  0.229 (Depositor), 0.234 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.188 (DCC) 
• R-Value Observed: 0.185 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.78	α = 90
b = 131.57	β = 107.36
c = 46.06	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SBC-Collect	data collection
DIALS	data reduction
xia2	data reduction
Aimless	data scaling
HKL-3000	phasing
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-05-15 
Deposition Author(s): Kim, Y., Stogios, P., Skarina, T., Di, R., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	--

Revision History  

• Version 1.0: 2019-05-15
  Type: Initial release
  
• Version 1.1: 2019-12-18
  Changes: Author supporting evidence
• Version 1.2: 2023-10-11
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-10-23
  Changes: Structure summary