2NSP

Crystal structure of pectin methylesterase D178A mutant in complex with hexasaccharide I

• PDB DOI: https://doi.org/10.2210/pdb2NSP/pdb

• Classification: HYDROLASE
• Organism(s): Dickeya dadantii 3937
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2006-11-06 Released: 2007-09-18 
• Deposition Author(s): Fries, M., Brocklehurst, K., Shevchik, V.E., Pickersgill, R.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.204 
• R-Value Work: 0.189 
• R-Value Observed: 0.189 

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: 76.13 kDa 
• Atom Count: 6,153 
• Modelled Residue Count: 684 
• Deposited Residue Count: 684 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pectinesterase A	A, B	342	Dickeya dadantii 3937	Mutation(s): 1  Gene Names: pemA, pem EC: 3.1.1.11
UniProt
Find proteins for P0C1A9 (Dickeya dadantii (strain 3937)) Explore P0C1A9  Go to UniProtKB:  P0C1A9

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
methyl alpha-D-galactopyranuronate-(1-4)-methyl alpha-D-galactopyranuronate-(1-4)-alpha-D-galactopyranuronic acid-(1-4)-alpha-D-galactopyranuronic acid-(1-4)-alpha-D-galactopyranuronic acid-(1-4)-methyl alpha-D-galactopyranuronate	C, D	6		N/A
Glycosylation Resources
GlyTouCan:  G87950TF GlyCosmos:  G87950TF

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.204 
• R-Value Work: 0.189 
• R-Value Observed: 0.189 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.11	α = 90
b = 85.103	β = 93.48
c = 97.281	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
ADSC	data collection
MOSFLM	data reduction
SCALA	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-09-18 
Deposition Author(s): Fries, M., Brocklehurst, K., Shevchik, V.E., Pickersgill, R.W.

Revision History  

• Version 1.0: 2007-09-18
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 2.0: 2020-05-13
  Changes: Advisory, Atomic model, Data collection, Derived calculations
• Version 3.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 3.1: 2021-10-20
  Changes: Database references, Derived calculations, Structure summary
• Version 3.2: 2023-08-30
  Changes: Data collection, Refinement description