7TRO | pdb_00007tro

Crystal structure of R14A-R20A human Galectin-7 mutant in presence of lactose

• PDB DOI: https://doi.org/10.2210/pdb7TRO/pdb

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


• Deposited: 2022-01-29 Released: 2023-02-01 
• 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), Fonds de Recherche du Quebec - Sante (FRQS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.221 (Depositor), 0.221 (DCC) 
• R-Value Work: 
  0.175 (Depositor), 0.175 (DCC) 
• R-Value Observed: 
  0.178 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of R14A-R20A 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: 30.11 kDa 
• Atom Count: 2,379 
• Modeled Residue Count: 267 
• Deposited Residue Count: 270 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Galectin-7	A, B	135	Homo sapiens	Mutation(s): 2  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	D Interactions
beta-D-galactopyranose-(1-4)-beta-D-glucopyranose	C	2		N/A
Glycosylation Resources
GlyTouCan: G84224TW GlyCosmos: G84224TW GlyGen: G84224TW

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TRS	E [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
EDO	D [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_900004	C	beta-lactose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.221 (Depositor), 0.221 (DCC) 
• R-Value Work:  0.175 (Depositor), 0.175 (DCC) 
• R-Value Observed: 0.178 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.97	α = 90
b = 66.16	β = 90
c = 70.55	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: 2023-02-01 
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
Fonds de Recherche du Quebec - Sante (FRQS)	Canada	FRQ-S Research Scholar Senior Career Award (281993)
Fonds de Recherche du Quebec - Sante (FRQS)	Canada	FRQ-S Junior 1 (251848)
Natural Sciences and Engineering Research Council (NSERC, Canada)	Canada	RGPIN-2017-06091
Fonds de Recherche du Quebec - Sante (FRQS)	Canada	FRQ-S Doctoral Training scholarship (287239)

Revision History  

• Version 1.0: 2023-02-01
  Type: Initial release
  
• Version 1.1: 2023-10-25
  Changes: Data collection, Refinement description