3R5X | pdb_00003r5x

Crystal Structure of D-alanine--D-Alanine Ligase from Bacillus anthracis complexed with ATP

• PDB DOI: https://doi.org/10.2210/pdb3R5X/pdb

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


• Deposited: 2011-03-20 Released: 2011-04-06 
• 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: 2.00 Å
• R-Value Free: 
  0.221 (Depositor), 0.218 (DCC) 
• R-Value Work: 
  0.177 (Depositor), 0.174 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

Literature

Crystal Structure of D-alanine--D-Alanine Ligase from Bacillus anthracis complexed with ATP

Kim, Y., 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)

Biological Assembly 2  

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

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

Macromolecule Content 

• Total Structure Weight: 141.73 kDa 
• Atom Count: 10,379 
• Modeled Residue Count: 1,183 
• Deposited Residue Count: 1,228 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-alanine--D-alanine ligase	A, B, C, D	307	Bacillus anthracis	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 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP	F [auth A], H [auth B], K [auth C], O [auth D]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
EDO	Q [auth D]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACY	R [auth D]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N
CA	E [auth A], G [auth B], I [auth B], J [auth C], L [auth C], N [auth D], P [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG	M [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.221 (Depositor), 0.218 (DCC) 
• R-Value Work:  0.177 (Depositor), 0.174 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m33r5x

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.336	α = 73.36
b = 68.992	β = 84.96
c = 92.387	γ = 75.46

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-04-06 
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: 2011-04-06
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2014-10-01
  Changes: Database references, Structure summary
• Version 1.3: 2015-06-24
  Changes: Other
• Version 1.4: 2015-07-01
  Changes: Derived calculations
• Version 1.5: 2024-11-27
  Changes: Data collection, Database references, Derived calculations, Structure summary