1BN8 | pdb_00001bn8

BACILLUS SUBTILIS PECTATE LYASE

• PDB DOI: https://doi.org/10.2210/pdb1BN8/pdb

• Classification: LYASE
• Organism(s): Bacillus subtilis
• Mutation(s): No 


• Deposited: 1998-07-31 Released: 1998-08-05 
• Deposition Author(s): Pickersgill, R., Harris, G., Jenkins, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Work: 
  0.179 (Depositor), 0.163 (DCC) 

Literature

The structure of Bacillus subtilis pectate lyase in complex with calcium.

Pickersgill, R., Jenkins, J., Harris, G., Nasser, W., Robert-Baudouy, J.

(1994) Nat Struct Biol 1: 717-723

• PubMed: 7634076 
• DOI: https://doi.org/10.1038/nsb1094-717
• Primary Citation Related Structures: 
  1BN8


• PubMed Abstract: 
  

  We have solved the structure of the Bacillus subtilis pectate lyase (BsPel) in complex with calcium. The structure consists of a parallel beta-helix domain and a loop region. The alpha L-bounded beta-strand seen in BsPel is a new element of protein structure and its frequent occurrence suggests it is an important characteristic of the parallel beta-helix. A pronounced cleft is formed between the loops and the parallel beta-helix domain and we propose that this is the active site cleft. Calcium, essential for the activity of the enzyme, binds at the bottom of this cleft and an arginine residue close to the calcium, which is conserved across all pectin and pectate lyases, may be involved in catalysis.

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Organizational Affiliation: 
• Department of Protein Engineering, Institute of Food Research, Reading, UK.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 45.59 kDa 
• Atom Count: 3,276 
• Modeled Residue Count: 399 
• Deposited Residue Count: 420 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (PECTATE LYASE)	A	420	Bacillus subtilis	Mutation(s): 0  EC: 4.2.2.2
UniProt
Find proteins for P39116 (Bacillus subtilis (strain 168)) Explore P39116  Go to UniProtKB:  P39116

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: 1.80 Å
• R-Value Work:  0.179 (Depositor), 0.163 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.9	α = 90
b = 89	β = 108.93
c = 50.7	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-08-05 
Deposition Author(s): Pickersgill, R., Harris, G., Jenkins, J.

Revision History  

• Version 1.0: 1998-08-05
  Type: Initial release
  
• Version 1.1: 2007-10-16
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-07
  Changes: Data collection, Database references, Derived calculations