3A5F

High-resolution structure of DHDPS from Clostridium botulinum in complex with pyruvate

• PDB DOI: https://doi.org/10.2210/pdb3A5F/pdb

• Classification: LYASE
• Organism(s): Clostridium botulinum A str. ATCC 19397
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2009-08-06 Released: 2010-06-30 
• Deposition Author(s): Atkinson, S.C., Dobson, R.C.J., Perugini, M.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.19 Å
• R-Value Free: 0.140 
• R-Value Work: 0.112 
• R-Value Observed: 0.113 

Literature

The high resolution structure of DHDPS from Clostridium botulinum

Dobson, R.C.J., Atkinson, S.C.

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: 63.43 kDa 
• Atom Count: 5,606 
• Modelled Residue Count: 582 
• Deposited Residue Count: 582 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydrodipicolinate synthase	A, B	291	Clostridium botulinum A str. ATCC 19397	Mutation(s): 0  Gene Names: dapA EC: 4.2.1.52

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A], D [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
KPI	A, B	L-PEPTIDE LINKING	C9 H16 N2 O4		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.19 Å
• R-Value Free: 0.140 
• R-Value Work: 0.112 
• R-Value Observed: 0.113 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 143.358	α = 90
b = 54.836	β = 126.29
c = 94.304	γ = 90

Software Package:

Software Name	Purpose
PHASES	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-06-30 
Deposition Author(s): Atkinson, S.C., Dobson, R.C.J., Perugini, M.A.

Revision History  

• Version 1.0: 2010-06-30
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2012-12-26
  Changes: Structure summary
• Version 1.3: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2023-11-29
  Changes: Data collection