3IRD | pdb_00003ird

Structure of dihydrodipicolinate synthase from Clostridium botulinum

• PDB DOI: https://doi.org/10.2210/pdb3IRD/pdb
• Entry: 3IRD supersedes: 3BI8

• Classification: LYASE
• Organism(s): Clostridium botulinum A str. Hall
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-08-22 Released: 2009-09-22 
• Deposition Author(s): Dobson, R.C.J., Atkinson, S., Perugini, M.A.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.23 Å
• R-Value Free: 
  0.209 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.135 (Depositor), 0.130 (DCC) 
• R-Value Observed: 
  0.142 (Depositor) 

Literature

Structure of Cbot-DHDPS

Atkinson, S., Dobson, R.C.J., Perugini, M.A.

To be published.

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: 31.96 kDa 
• Atom Count: 2,495 
• Modelled Residue Count: 291 
• Deposited Residue Count: 291 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydrodipicolinate synthase	A	291	Clostridium botulinum A str. Hall	Mutation(s): 0  Gene Names: dapA EC: 4.2.1.52 (PDB Primary Data), 4.3.3.7 (UniProt)
UniProt
Find proteins for A5I6N2 (Clostridium botulinum (strain Hall / ATCC 3502 / NCTC 13319 / Type A)) Explore A5I6N2  Go to UniProtKB:  A5I6N2

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MLT	B [auth A]	D-MALATE C4 H6 O5 BJEPYKJPYRNKOW-UWTATZPHSA-N
GOL	F [auth A], G [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	D [auth A], E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.23 Å
• R-Value Free:  0.209 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.135 (Depositor), 0.130 (DCC) 
• R-Value Observed: 0.142 (Depositor) 

Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.81	α = 90
b = 92.81	β = 90
c = 60.35	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-09-22 
Deposition Author(s): Dobson, R.C.J., Atkinson, S., Perugini, M.A.
• This entry supersedes: 3BI8

Revision History  

• Version 1.0: 2009-09-22
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2018-06-20
  Changes: Data collection, Database references
• Version 1.3: 2024-03-20
  Changes: Data collection, Database references, Derived calculations