4HWV | pdb_00004hwv

Structure of Pectate Lyase from Acidovorax avenae subsp citrulli

• PDB DOI: https://doi.org/10.2210/pdb4HWV/pdb

• Classification: LYASE
• Organism(s): Paracidovorax citrulli AAC00-1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-11-09 Released: 2013-10-23 
• Deposition Author(s): Qun, T., Liqun, Z.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.37 Å
• R-Value Free: 
  0.149 (Depositor), 0.128 (DCC) 
• R-Value Work: 
  0.124 (Depositor), 0.128 (DCC) 
• R-Value Observed: 
  0.126 (Depositor) 

Literature

1.37 angstrom crystal structure of pathogenic factor pectate lyase from Acidovorax citrulli.

Tang, Q., Liu, Y.P., Ren, Z.G., Yan, X.X., Zhang, L.Q.

(2013) Proteins 81: 1485-1490

• PubMed: 23568384 
• DOI: https://doi.org/10.1002/prot.24298
• Primary Citation Related Structures: 
  4HWV


• PubMed Abstract: 
  

  Pectates lyase (Pel) plays an important role in bacteria pathogenicity. The crystal structure of Pel from Acidovorax citrulli (AcPel) has been solved to 1.37 Å resolution. AcPel belongs to the polysaccharide lyase family 1 (PL1), which has a characteristic right-handed β-helix fold. AcPel is similar with other Pels in the PL1 family, but also shows some differences at the substrate binding site.

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Organizational Affiliation: 
• Department of Plant Pathology, China Agricultural University, Beijing, China.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 108.27 kDa 
• Atom Count: 9,264 
• Modeled Residue Count: 985 
• Deposited Residue Count: 1,006 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pectate lyase/Amb allergen	A, B	503	Paracidovorax citrulli AAC00-1	Mutation(s): 0  Gene Names: Aave_3434
UniProt
Find proteins for A1TSQ3 (Paracidovorax citrulli (strain AAC00-1)) Explore A1TSQ3  Go to UniProtKB:  A1TSQ3

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.37 Å
• R-Value Free:  0.149 (Depositor), 0.128 (DCC) 
• R-Value Work:  0.124 (Depositor), 0.128 (DCC) 
• R-Value Observed: 0.126 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.676	α = 90
b = 71.872	β = 92.71
c = 90.953	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASES	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-10-23 
Deposition Author(s): Qun, T., Liqun, Z.

Revision History  

• Version 1.0: 2013-10-23
  Type: Initial release
  
• Version 1.1: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary