1EE6 | pdb_00001ee6

CRYSTAL STRUCTURE OF PECTATE LYASE FROM BACILLUS SP. STRAIN KSM-P15.

• PDB DOI: https://doi.org/10.2210/pdb1EE6/pdb

• Classification: LYASE
• Organism(s): Bacillus sp. KSM-P15
• Mutation(s): No 


• Deposited: 2000-01-31 Released: 2001-01-31 
• Deposition Author(s): Akita, M., Suzuki, A., Kobayashi, T., Ito, S., Yamane, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.234 (Depositor) 
• R-Value Work: 
  0.186 (Depositor) 

Literature

The first structure of pectate lyase belonging to polysaccharide lyase family 3.

Akita, M., Suzuki, A., Kobayashi, T., Ito, S., Yamane, T.

(2001) Acta Crystallogr D Biol Crystallogr 57: 1786-1792

• PubMed: 11717490 
• DOI: https://doi.org/10.1107/s0907444901014482
• Primary Citation Related Structures: 
  1EE6


• PubMed Abstract: 
  

  The crystal structure of a highly alkaline low molecular weight pectate lyase (Pel-15) was determined at 1.5 A resolution by the multiple isomorphous replacement (MIR) method. This is the first pectate lyase structure from polysaccharide lyase family 3. The overall structure is a simple eight-turn right-handed parallel beta-helix domain with one long loop protruding from one side of the beta-helix. The low molecular weight of Pel-15 derives from the lack of N- and C-terminal extensions that are found in many beta-helix proteins. Although the structure has one calcium ion at pH 6.7, raising the pH to 9.5 results in the binding of an additional calcium ion. The common calcium ion found in both the pH 6.5 and 9.5 structures seems to stabilize both the beta-helix structure and the long protruding loop. The additional calcium ion found in the pH 9.5 structure alone may neutralize the acidic substrate. The region around the additional calcium ion is thought to bind to the substrate, as this region is rich in charged amino-acid residues which are required in catalysis.

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Organizational Affiliation: 
• Department of Biotechnology and Biomaterial Chemistry, Graduate School of Engineering, Nagoya University, Chikusa-ku, Nagoya 464-8603, Japan. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 20.99 kDa 
• Atom Count: 1,643 
• Modeled Residue Count: 197 
• Deposited Residue Count: 197 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PECTATE LYASE	A	197	Bacillus sp. KSM-P15	Mutation(s): 0  EC: 4.2.2.2
UniProt
Find proteins for A0ACD6B936 (Bacillus sp) Explore A0ACD6B936  Go to UniProtKB:  A0ACD6B936

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.234 (Depositor) 
• R-Value Work:  0.186 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.9	α = 90
b = 60.5	β = 90
c = 83	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MLPHARE	phasing
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-01-31 
Deposition Author(s): Akita, M., Suzuki, A., Kobayashi, T., Ito, S., Yamane, T.

Revision History  

• Version 1.0: 2001-01-31
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary