6RGU

Photorhabdus asymbiotica lectin PHL in complex with 3-O-methyl-D-glucose

• PDB DOI: https://doi.org/10.2210/pdb6RGU/pdb

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


• Deposited: 2019-04-17 Released: 2020-07-01 
• Deposition Author(s): Houser, J., Fujdiarova, E., Jancarikova, G., Wimmerova, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.197 
• R-Value Work: 0.169 
• R-Value Observed: 0.170 

Biological Assembly 1  

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

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

Biological Assembly Evidence: equilibrium centrifugation

Macromolecule Content

• Total Structure Weight: 42.01 kDa 
• Atom Count: 3,097 
• Modelled Residue Count: 345 
• Deposited Residue Count: 369 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lectin PHL	A	369	Photorhabdus asymbiotica	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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3MG	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	3-O-methyl-beta-D-glucopyranose C7 H14 O6 SCBBSJMAPKXHAH-BNWJMWRWSA-N
CL	J [auth A], K [auth A], L [auth A], M [auth A], N [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	O [auth A], P [auth A], Q [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
3MG	Binding MOAD:  6RGU	Kd: 1.41e+7 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.197 
• R-Value Work: 0.169 
• R-Value Observed: 0.170 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.828	α = 90
b = 80.828	β = 90
c = 113.243	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: 2020-07-01 
Deposition Author(s): Houser, J., Fujdiarova, E., Jancarikova, G., Wimmerova, M.

Revision History  

• Version 1.0: 2020-07-01
  Type: Initial release
  
• Version 1.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations
• Version 1.2: 2021-02-24
  Changes: Database references, Structure summary
• Version 1.3: 2024-01-24
  Changes: Data collection, Database references, Refinement description