1PE9 | pdb_00001pe9

MUTATIONS IN THE T1.5 LOOP OF PECTATE LYASE A

• PDB DOI: https://doi.org/10.2210/pdb1PE9/pdb

• Classification: LYASE
• Organism(s): Dickeya chrysanthemi
• Expression System: Escherichia coli
• Mutation(s): Yes 
• Membrane Protein: Yes  OPM


• Deposited: 2003-05-21 Released: 2004-03-16 
• Deposition Author(s): Dehdashti, S.J., Doan, C.N., Chao, K.L., Yoder, M.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.213 (Depositor), 0.213 (DCC) 
• R-Value Work: 
  0.198 (Depositor), 0.198 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Starting Model: experimental

Literature

Effect of mutations in the T1.5 loop of pectate lyase A from Erwinia chrysanthemi EC16.

Dehdashti, S.J., Doan, C.N., Chao, K.L., Yoder, M.D.

(2003) Acta Crystallogr D Biol Crystallogr 59: 1339-1342

• PubMed: 12832805 
• DOI: https://doi.org/10.1107/s0907444903011491
• Primary Citation Related Structures: 
  1OOC, 1PE9


• PubMed Abstract: 
  

  Pectate lyase A (PelA) is a pectate-degrading enzyme secreted by plant pathogens. PelA from Erwinia chrysanthemi has 61% amino-acid identity and a conserved structural similarity to pectate lyase E (PelE). Although similar in structure and sequence, the enzymatic characteristics of PelA differ from those for PelE. A structural alignment of PelA and PelE reveals differences in the T1.5 loop. The sequence of the T1.5 loop in PelA was mutated to the homologous sequence in PelE. The crystal structure of the PelA T1.5 mutant has been solved to 1.6 and 2.9 A resolution. The enzymatic and structural properties of the T1.5 mutant are discussed.

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Organizational Affiliation: 
• University of Missouri Kansas City, School of Biological Sciences, 5100 Rockhill Road, Kansas City, Missouri 64111-2499, USA.

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: 77.48 kDa 
• Atom Count: 6,230 
• Modeled Residue Count: 722 
• Deposited Residue Count: 722 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pectate lyase A	A, B	361	Dickeya chrysanthemi	Mutation(s): 4  Gene Names: PELA EC: 4.2.2.2 Membrane Entity: Yes
UniProt
Find proteins for P0C1A2 (Dickeya chrysanthemi) Explore P0C1A2  Go to UniProtKB:  P0C1A2

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.213 (Depositor), 0.213 (DCC) 
• R-Value Work:  0.198 (Depositor), 0.198 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.797	α = 90
b = 154.04	β = 90
c = 51.129	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-03-16 
Deposition Author(s): Dehdashti, S.J., Doan, C.N., Chao, K.L., Yoder, M.D.

Revision History  

• Version 1.0: 2004-03-16
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2015-07-29
  Changes: Other
• Version 1.4: 2023-08-16
  Changes: Data collection, Database references, Refinement description
• Version 1.5: 2024-11-20
  Changes: Structure summary