Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 37773.68 
• Atom Count: 2650 
• Residue Count: 353 
• Unique protein chains: 1

1O8F

Pectate Lyase C from Erwinia Chrysanthemi at pH 9.5 with 30mM Ca2+

• DOI: 10.2210/pdb1O8F/pdb

• Classification: HYDROLASE
• Organism(s): Dickeya chrysanthemi
• Expression System: Escherichia coli


• Deposited: 2002-11-27 Released: 2003-01-30 
• Deposition Author(s): Herron, S.R., Jurnak, F.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.2 Å
• R-Value Free: 0.230 
• R-Value Work: 0.184 

Literature

Characterization and Implications of Ca2+ Binding to Pectate Lyase C

Herron, S.R., Scavetta, R., Garrett, M., Legner, M., Jurnak, F.A.

(2003) J.Biol.Chem. 278: 12271-12277

• PubMed: 12540845 
• DOI: 10.1074/jbc.M209306200
• Primary Citation of Related Structures:  
  1O8M, 1O8L, 1O8K, 1O8J, 1O8I, 1O8H, 1O8G, 1O8E, 1O8D, 1O88


• PubMed Abstract: 
  

Ca(2+) is essential for in vitro activity of Erwinia chrysanthemi pectate lyase C (PelC). Crystallographic analyses of 11 PelC-Ca(2+) complexes, formed at pH 4.5, 9.5, and 11.2 under varying Ca(2+) concentrations, have been solved and refined at a resolution of 2.2 A. The Ca(2+) site represents a new motif for Ca(2+), consisting primarily of beta-turns and beta-strands. The principal differences between PelC and the PelC-Ca(2+) structures at all pH values are the side-chain conformations of Asp-129 and Glu-166 as well as the occupancies of four water molecules. According to calculations of pK(a) values, the presence of Ca(2+) and associated structural changes lower the pK(a) of Arg-218, the amino acid responsible for proton abstraction during catalysis. The Ca(2+) affinity for PelC is weak, as the K(d) was estimated to be 0.132 (+/-0.004) mm at pH 9.5, 1.09 (+/-0.29) mm at pH 11.2, and 5.84 (+/-0.41) mm at pH 4.5 from x-ray diffraction studies and 0.133 (+/-0.045) mm at pH 9.5 from intrinsic tryptophan fluorescence measurements. Given the pH dependence of Ca(2+) affinity, PelC activity at pH 4.5 has been reexamined. At saturating Ca(2+) concentrations, PelC activity increases 10-fold at pH 4.5 but is less than 1% of maximal activity at pH 9.5. Taken together, the studies suggest that the primary Ca(2+) ion in PelC has multiple functions.

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Organizational Affiliation: 

Department of Physiology and Biophysics, University of California, Irvine, California 92697-4560, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
PECTATE LYASE C	A	353	Dickeya chrysanthemi	Mutation(s): 0  Gene Names: pelC EC: 4.2.2.2
Find proteins for P11073 (Dickeya chrysanthemi) Go to UniProtKB:  P11073

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
CA	A	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.2 Å
• R-Value Free: 0.230 
• R-Value Work: 0.184 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 72.710	α = 90.00
b = 80.800	β = 90.00
c = 95.740	γ = 90.00

Software Package:

Software Name	Purpose
SDMS	data reduction
X-PLOR	phasing
X-PLOR	refinement
SDMS	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-11-27 
• Released Date: 2003-01-30 
• Deposition Author(s): Herron, S.R., Jurnak, F.A.

Revision History 

• Version 1.0: 2003-01-30
  Type: Initial release
• Version 1.1: 2011-05-08
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance
• Version 1.3: 2018-06-13
  Type: Data collection, Database references, Structure summary