1JTA

Crystal Structure of Pectate Lyase A (C2 form)

• PDB DOI: https://doi.org/10.2210/pdb1JTA/pdb

• Classification: LYASE
• Organism(s): Dickeya chrysanthemi
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2001-08-20 Released: 2002-06-19 
• Deposition Author(s): Thomas, L.M., Doan, C.N., Oliver, R.L., Yoder, M.D.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.225 
• R-Value Work: 0.181 
• R-Value Observed: 0.181 

Starting Model: experimental

Literature

Structure of pectate lyase A: comparison to other isoforms.

Thomas, L.M., Doan, C.N., Oliver, R.L., Yoder, M.D.

(2002) Acta Crystallogr D Biol Crystallogr 58: 1008-1015

• PubMed: 12037303 
• DOI: https://doi.org/10.1107/s0907444902005851
• Primary Citation of Related Structures:  
  1JRG, 1JTA


• PubMed Abstract: 
  

  Pectate lyase A is a virulence factor secreted by the plant-pathogenic bacteria Erwinia chrysanthemi. The enzyme cleaves the glycosidic bond of pectate polymers by a calcium-dependent beta-elimination mechanism. The crystal structure of pectate lyase A from E. chrysanthemi EC16 has been determined in two crystal forms, monoclinic C2 to 1.8 A and rhombohedral R3 to 2.1 A. The protein structure is compared with two other pectate lyase isoforms from E. chrysanthemi EC16, pectate lyase C and pectate lyase E. Pectate lyase A is unique as it is the only acidic pectate lyase and has end products that are significantly more varied in length in comparison to those of the other four major pectate lyase isozymes. Differences and similarities in polypeptide trace, size and volume of the active-site groove and surface electrostatics are discussed.

---

Organizational Affiliation: 

School of Biological Sciences, University of Missouri-Kansas City, 5007 Rockhill Road, Kansas City, MO 64110-2499, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 38.89 kDa 
• Atom Count: 2,967 
• Modelled Residue Count: 361 
• Deposited Residue Count: 361 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
pectate lyase A	A	361	Dickeya chrysanthemi	Mutation(s): 0  Gene Names: pelA EC: 4.2.2.2
UniProt
Find proteins for P0C1A2 (Dickeya chrysanthemi) Explore P0C1A2  Go to UniProtKB:  P0C1A2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.225 
• R-Value Work: 0.181 
• R-Value Observed: 0.181 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.549	α = 90
b = 53.802	β = 109.45
c = 71.039	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-06-19 
Deposition Author(s): Thomas, L.M., Doan, C.N., Oliver, R.L., Yoder, M.D.

Revision History  

• Version 1.0: 2002-06-19
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-04-03
  Changes: Data collection, Database references, Derived calculations, Refinement description