7N8D | pdb_00007n8d

Crystal structure of R22A human Galectin-7 mutant in presence of Lactose

• PDB DOI: https://doi.org/10.2210/pdb7N8D/pdb

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


• Deposited: 2021-06-14 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: 2.49 Å
• R-Value Free: 
  0.281 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.242 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.244 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of R22A 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.

Macromolecule Content 

• Total Structure Weight: 30.52 kDa 
• Atom Count: 2,321 
• Modeled Residue Count: 268 
• Deposited Residue Count: 270 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Galectin-7	A	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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Galectin-7	B	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: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose	C [auth D], D [auth E]	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	E [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO	B	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900008	C [auth D], D [auth E]	alpha-lactose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.49 Å
• R-Value Free:  0.281 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.242 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.244 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 30.53	α = 90
b = 77.62	β = 90
c = 111.95	γ = 90

Software Package:

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

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
• Version 1.2: 2023-11-15
  Changes: Data collection
• Version 1.3: 2024-11-06
  Changes: Structure summary