4Z3F

Crystal structure of the lectin domain of PapG from E. coli BI47 in complex with SSEA4 in space group P21

• PDB DOI: https://doi.org/10.2210/pdb4Z3F/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Escherichia coli
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-03-31 Released: 2016-04-13 
• Deposition Author(s): Jakob, R.P., Navarra, G., Zihlmann, P., Stangier, K., Preston, R.C., Rabbani, S., Maier, T., Ernst, B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.225 
• R-Value Work: 0.201 
• R-Value Observed: 0.202 

Literature

An unexpected way nature improves solvation entropy

Navarra, G., Zihlmann, P., Jakob, R.P., Stangier, K., Preston, R.C., Rabbani, S., Maier, T., Ernst, B.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 24.05 kDa 
• Atom Count: 1,893 
• Modelled Residue Count: 197 
• Deposited Residue Count: 198 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PapG, lectin domain	A	198	Escherichia coli	Mutation(s): 0  Gene Names: G801_04654, G801_04690
UniProt
Find proteins for A0A182DW20 (Escherichia coli) Explore A0A182DW20  Go to UniProtKB:  A0A182DW20

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-3)-alpha-D-galactopyranose-(1-4)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose	B	6		N/A
Glycosylation Resources
GlyTouCan:  G32254QI GlyCosmos:  G32254QI GlyGen:  G32254QI

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A], D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.225 
• R-Value Work: 0.201 
• R-Value Observed: 0.202 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.11	α = 90
b = 53.38	β = 96.05
c = 48.82	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-04-13 
Deposition Author(s): Jakob, R.P., Navarra, G., Zihlmann, P., Stangier, K., Preston, R.C., Rabbani, S., Maier, T., Ernst, B.

Revision History  

• Version 1.0: 2016-04-13
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary