4U4B

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

• PDB DOI: https://doi.org/10.2210/pdb4U4B/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.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.250 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.170 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.174 (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., Schevchik, 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 and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 37.37 kDa 
• Atom Count: 2,630 
• Modelled Residue Count: 326 
• Deposited Residue Count: 347 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pectate lyase	A	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.250 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.170 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.174 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37	α = 90
b = 44.35	β = 93.58
c = 86.25	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

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

Revision History  

• Version 1.0: 2015-08-05
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-11-20
  Changes: Structure summary