3DEB | pdb_00003deb

Crystal Structure of apo form (Zinc removed) of the Botulinum Neurotoxin Type C Light Chain

• PDB DOI: https://doi.org/10.2210/pdb3DEB/pdb

• Classification: HYDROLASE
• Organism(s): Clostridium botulinum
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-06-09 Released: 2009-04-07 
• Deposition Author(s): Rawat, R., Kumaran, D., Swaminathan, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.200 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.193 (DCC) 
• R-Value Observed: 
  0.194 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of apo form (Zinc removed) of the Botulinum Neurotoxin Type C Light Chain

Rawat, R., Kumaran, D., Swaminathan, S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 51.95 kDa 
• Atom Count: 3,989 
• Modeled Residue Count: 432 
• Deposited Residue Count: 450 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Botulinum neurotoxin C1 light chain	A	450	Clostridium botulinum	Mutation(s): 0  Gene Names: BoNT/C EC: 3.4.24.69
UniProt
Find proteins for P18640 (Clostridium botulinum C phage) Explore P18640  Go to UniProtKB:  P18640

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACT	D [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
FMT	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N
CA	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
NA	B [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.200 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.193 (DCC) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.74	α = 90
b = 106.74	β = 90
c = 140.24	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
CBASS	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-04-07 
Deposition Author(s): Rawat, R., Kumaran, D., Swaminathan, S.

Revision History  

• Version 1.0: 2009-04-07
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description