Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 34500.22 
• Atom Count: 2462 
• Residue Count: 319 
• Unique protein chains: 1

1GQ8

Pectin methylesterase from Carrot

• DOI: 10.2210/pdb1GQ8/pdb

• Classification: HYDROLASE
• Organism(s): Daucus carota


• Deposited: 2001-11-20 Released: 2002-04-18 
• Deposition Author(s): Johansson, K., El-Ahmad, M., Friemann, R., Jornvall, H., Markovic, O., Eklund, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.193 
• R-Value Work: 0.181 

Literature

Crystal Structure of Plant Pectin Methylesterase

Johansson, K., El-Ahmad, M., Friemann, R., Jornvall, H., Markovic, O., Eklund, H.

(2002) FEBS Lett. 514: 243

• PubMed: 11943159 


• PubMed Abstract: 
  

Pectin is a principal component in the primary cell wall of plants. During cell development, pectin is modified by pectin methylesterases to give different properties to the cell wall. This report describes the first crystal structure of a plant pectin methylesterase. The beta-helical structure embodies a central cleft, lined by several aromatic residues, that has been deduced to be suitable for pectin binding. The active site is found at the center of this cleft where Asp157 is suggested to act as the nucleophile, Asp136 as an acid/base and Gln113/Gln135 to form an anion hole to stabilize the transition state.

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Organizational Affiliation: 

Department of Molecular Biology, Swedish University of Agricultural Sciences, S-751 24 Uppsala, Sweden.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
PECTINESTERASE	A	319	Daucus carota	Mutation(s): 0  EC: 3.1.1.11
Find proteins for P83218 (Daucus carota) Go to UniProtKB:  P83218

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
CAC	A	CACODYLATE ION dimethylarsinate C2 H6 As O2 OGGXGZAMXPVRFZ-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PCA	A	L-PEPTIDE LINKING	C5 H7 N O3		GLU

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.193 
• R-Value Work: 0.181 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length (Å)	Angle (°)
a = 77.690	α = 90.00
b = 89.410	β = 90.00
c = 49.500	γ = 90.00

Software Package:

Software Name	Purpose
AMoRE	phasing
MOSFLM	data reduction
CNS	refinement
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2001-11-20 
• Released Date: 2002-04-18 
• Deposition Author(s): Johansson, K., El-Ahmad, M., Friemann, R., Jornvall, H., Markovic, O., Eklund, H.

Revision History 

• Version 1.0: 2002-04-18
  Type: Initial release
• Version 1.1: 2011-09-14
  Type: Database references, Derived calculations, Non-polymer description, Other, Refinement description, Structure summary, Version format compliance
• Version 1.2: 2018-01-17
  Type: Data collection