1XKY | pdb_00001xky

Crystal Structure of Dihydrodipicolinate Synthase DapA-2 (BA3935) from Bacillus Anthracis at 1.94A Resolution.

• PDB DOI: https://doi.org/10.2210/pdb1XKY/pdb

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


• Deposited: 2004-09-30 Released: 2005-10-04 
• Deposition Author(s): Levdikov, V., Blagova, E., Fogg, M.J., Brannigan, J.A., Milioti, N., Wilkinson, A.J., Wilson, K.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free: 
  0.197 (Depositor), 0.208 (DCC) 
• R-Value Work: 
  0.153 (Depositor), 0.167 (DCC) 
• R-Value Observed: 
  0.156 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of dihydrodipicolinate synthase (BA3935) from Bacillus anthracis at 1.94 A resolution

Blagova, E., Levdikov, V., Milioti, N., Fogg, M.J., Kalliomaa, A.K., Brannigan, J.A., Wilson, K.S., Wilkinson, A.J.

(2006) Proteins 62: 297-301

• PubMed: 16287120 
• DOI: https://doi.org/10.1002/prot.20684
• Primary Citation Related Structures: 
  1XKY, 1XL9

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Organizational Affiliation: 
• Department of Chemistry, University of York, York, United Kingdom.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 129.68 kDa 
• Atom Count: 10,516 
• Modeled Residue Count: 1,168 
• Deposited Residue Count: 1,204 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
dihydrodipicolinate synthase	A, B, C, D	301	Bacillus anthracis	Mutation(s): 0  Gene Names: DapA-2 EC: 4.2.1.52 (PDB Primary Data), 4.3.3.7 (UniProt)
UniProt
Find proteins for A0A6L7H340 (Bacillus anthracis) Explore A0A6L7H340  Go to UniProtKB:  A0A6L7H340

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
K	E [auth A], F [auth A], G [auth B], H [auth B], I [auth B], J [auth C], K [auth C], L [auth C], M [auth D], N [auth D]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free:  0.197 (Depositor), 0.208 (DCC) 
• R-Value Work:  0.153 (Depositor), 0.167 (DCC) 
• R-Value Observed: 0.156 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.203	α = 90
b = 126.882	β = 90
c = 173.319	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-10-04 
Deposition Author(s): Levdikov, V., Blagova, E., Fogg, M.J., Brannigan, J.A., Milioti, N., Wilkinson, A.J., Wilson, K.S.

Revision History  

• Version 1.0: 2005-10-04
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-23
  Changes: Data collection, Database references, Derived calculations, Refinement description