7RDG | pdb_00007rdg

Crystal structure of D103A human Galectin-7 mutant in presence of lactose

• PDB DOI: https://doi.org/10.2210/pdb7RDG/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2021-07-09 Released: 2023-01-25 
• Deposition Author(s): Pham, N.T.H., Calmettes, C., Doucet, N.
• Funding Organization(s): Natural Sciences and Engineering Research Council (NSERC, Canada), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Other government

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.268 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.204 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.210 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of D103A human Galectin-7 mutant in presence of lactose

Pham, N.T.H., Calmettes, C., Doucet, N.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 61.24 kDa 
• Atom Count: 4,372 
• Modeled Residue Count: 533 
• Deposited Residue Count: 540 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Galectin-7	A [auth C], B, C [auth A], D	135	Homo sapiens	Mutation(s): 1  Gene Names: LGALS7, PIG1, LGALS7B
UniProt & NIH Common Fund Data Resources
Find proteins for P47929 (Homo sapiens) Explore P47929  Go to UniProtKB:  P47929
PHAROS:  P47929 GTEx:  ENSG00000178934 ENSG00000205076

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose	E, F, G, H	2		N/A
Glycosylation Resources
GlyTouCan:  G88362QR GlyCosmos:  G88362QR GlyGen:  G88362QR

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	I [auth C], J [auth A], K [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900008	E, F, G, H	alpha-lactose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.268 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.204 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.210 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 30.33	α = 90
b = 112.28	β = 91.08
c = 77.04	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-01-25 
Deposition Author(s): Pham, N.T.H., Calmettes, C., Doucet, N.

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Funding Organization	Location	Grant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)	Canada	RGPIN 2016-05557
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM105978
Other government	Canada	Fonds de Recherche du Quebec - Sante (FRQ-S) - Research Scholar Senior Career Award (281993)
Other government	Canada	Fonds de Recherche du Quebec - Sante (FRQ-S) - Junior 1 (251848)
Natural Sciences and Engineering Research Council (NSERC, Canada)	Canada	RGPIN-2017-06091
Other government	Canada	Fonds de Recherche du Quebec - Sante (FRQ-S) - Doctoral Training scholarship (287239)

Revision History  

• Version 1.0: 2023-01-25
  Type: Initial release
  
• Version 1.1: 2023-10-25
  Changes: Data collection, Refinement description