4U49

Crystal structure of Pectate Lyase Pel3 from Pectobacterium carotovorum with two monomers in the A.U

• PDB DOI: https://doi.org/10.2210/pdb4U49/pdb

• Classification: LYASE
• Organism(s): Pectobacterium carotovorum
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-07-23 Released: 2015-08-05 
• Deposition Author(s): Ballut, L., Gouet, P., Shevchik, V.
• Funding Organization(s): French National Research Agency

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.214 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.177 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.179 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Pectate Lyase Pel3 from Pectobacterium carotovorum with one monomer in the A.U

Ballut, L., Gouet, P., Shevchik, V.E., Pineau, C., Guschinskaya, N.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 74.46 kDa 
• Atom Count: 5,479 
• Modelled Residue Count: 629 
• Deposited Residue Count: 694 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pectate lyase	A, B	347	Pectobacterium carotovorum	Mutation(s): 0  Gene Names: pel-3 EC: 4.2.2.2
UniProt
Find proteins for Q47465 (Pectobacterium carotovorum) Explore Q47465  Go to UniProtKB:  Q47465

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.214 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.177 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.179 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.6	α = 90
b = 72	β = 101.3
c = 83.7	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	phasing
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-08-05 
Deposition Author(s): Ballut, L., Gouet, P., Shevchik, V.

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Funding Organization	Location	Grant Number
French National Research Agency	France	ANR-10-BLAN-1531-SECPATH

Revision History  

• Version 1.0: 2015-08-05
  Type: Initial release
  
• Version 2.0: 2017-09-06
  Changes: Advisory, Atomic model, Author supporting evidence, Derived calculations
• Version 2.1: 2024-01-31
  Changes: Data collection, Database references, Refinement description
• Version 2.2: 2024-10-23
  Changes: Structure summary