5MXG

Photorhabdus asymbiotica lectin (PHL) in complex with blood group H trisaccharide

• PDB DOI: https://doi.org/10.2210/pdb5MXG/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Photorhabdus asymbiotica subsp. asymbiotica ATCC 43949
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-01-23 Released: 2017-08-09 
• Deposition Author(s): Jancarikova, G., Houser, J., Demo, G., Wimmerova, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.228 
• R-Value Work: 0.185 
• R-Value Observed: 0.187 

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 41.82 kDa 
• Atom Count: 2,878 
• Modelled Residue Count: 344 
• Deposited Residue Count: 369 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Photorhabdus asymbiotica lectin PHL	A	369	Photorhabdus asymbiotica subsp. asymbiotica ATCC 43949	Mutation(s): 0  Gene Names: PAU_00698
UniProt
Find proteins for C7BLE4 (Photorhabdus asymbiotica subsp. asymbiotica (strain ATCC 43949 / 3105-77)) Explore C7BLE4  Go to UniProtKB:  C7BLE4

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B, C, D	3		N/A
Glycosylation Resources
GlyTouCan:  G61459JW GlyCosmos:  G61459JW GlyGen:  G61459JW

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NA	E [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900036	B, C, D	H type 2 antigen, beta anomer	Oligosaccharide / Antigen

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.228 
• R-Value Work: 0.185 
• R-Value Observed: 0.187 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.309	α = 90
b = 80.309	β = 90
c = 112.973	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-08-09 
Deposition Author(s): Jancarikova, G., Houser, J., Demo, G., Wimmerova, M.

Revision History  

• Version 1.0: 2017-08-09
  Type: Initial release
  
• Version 1.1: 2017-08-23
  Changes: Database references
• Version 1.2: 2018-01-24
  Changes: Source and taxonomy
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2024-01-17
  Changes: Data collection, Database references, Refinement description, Structure summary