2O04

Pectate lyase bound to hexasaccharide compound II

• PDB DOI: https://doi.org/10.2210/pdb2O04/pdb

• Classification: LYASE
• Organism(s): Bacillus subtilis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2006-11-27 Released: 2007-11-20 
• Deposition Author(s): Pickersgill, R.W., Seyedarabi, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.201 
• R-Value Work: 0.166 
• R-Value Observed: 0.168 

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 43.85 kDa 
• Atom Count: 3,670 
• Modelled Residue Count: 399 
• Deposited Residue Count: 399 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pectate lyase	A	399	Bacillus subtilis	Mutation(s): 1  Gene Names: pel EC: 4.2.2.2
UniProt
Find proteins for P39116 (Bacillus subtilis (strain 168)) Explore P39116  Go to UniProtKB:  P39116

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-galactopyranuronic acid-(1-4)-alpha-D-galactopyranuronic acid	B	2		N/A
Glycosylation Resources
GlyTouCan:  G65215OP GlyCosmos:  G65215OP

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.201 
• R-Value Work: 0.166 
• R-Value Observed: 0.168 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.619	α = 90
b = 68.879	β = 113.14
c = 59.459	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
ADSC	data collection
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-11-20 
Deposition Author(s): Pickersgill, R.W., Seyedarabi, A.

Revision History  

• Version 1.0: 2007-11-20
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2021-10-20
  Changes: Database references, Structure summary
• Version 2.2: 2023-12-27
  Changes: Data collection