3R23 | pdb_00003r23

Crystal Structure of D-alanine--D-Alanine Ligase from Bacillus anthracis

• PDB DOI: https://doi.org/10.2210/pdb3R23/pdb

• Classification: LIGASE
• Organism(s): Bacillus anthracis str. Ames
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2011-03-12 Released: 2011-03-30 
• Deposition Author(s): Kim, Y., Mulligan, R., Hasseman, J., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.256 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.188 (DCC) 
• R-Value Observed: 
  0.197 (Depositor) 

Literature

Crystal Structure of D-alanine--D-Alanine Ligase from Bacillus anthracis

Kim, Y., Mulligan, R., Hasseman, J., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 69.88 kDa 
• Atom Count: 4,989 
• Modeled Residue Count: 604 
• Deposited Residue Count: 614 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-alanine--D-alanine ligase	A, B	307	Bacillus anthracis str. Ames	Mutation(s): 0  Gene Names: BAS2435, BA_2610, ddl, ddlB, GBAA_2610 EC: 6.3.2.4
UniProt
Find proteins for Q81Q29 (Bacillus anthracis) Explore Q81Q29  Go to UniProtKB:  Q81Q29

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	C [auth A], D [auth A], E [auth B], F [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	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:  0.256 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.188 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m33r23

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.878	α = 90
b = 83.187	β = 90
c = 128.38	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	data collection
HKL-3000	phasing
PHENIX	model building
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-03-30 
Deposition Author(s): Kim, Y., Mulligan, R., Hasseman, J., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2011-03-30
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary