4NO4 | pdb_00004no4

Crystal Structure of Galectin-1 L11A mutant

• PDB DOI: https://doi.org/10.2210/pdb4NO4/pdb

• Classification: APOPTOSIS
• Organism(s): Rattus norvegicus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2013-11-19 Released: 2014-12-03 
• Deposition Author(s): Dessau, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.197 (Depositor), 0.196 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.188 (DCC) 
• R-Value Observed: 
  0.188 (Depositor) 

Literature

Crystal Structure of Galectin-1 L11A mutant

Dessau, M., Segev, O.

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.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 91.07 kDa 
• Atom Count: 7,753 
• Modeled Residue Count: 804 
• Deposited Residue Count: 804 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Galectin-1	A, B, C, D, E, F	134	Rattus norvegicus	Mutation(s): 1  Gene Names: Lgals1
UniProt
Find proteins for P11762 (Rattus norvegicus) Explore P11762  Go to UniProtKB:  P11762

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-galactopyranose-(1-4)-beta-D-glucopyranose	G, H, I, J, K, L	2		N/A
Glycosylation Resources
GlyTouCan: G84224TW GlyCosmos: G84224TW GlyGen: G84224TW

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	N [auth A], T [auth E]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	O [auth A], P [auth A], Q [auth B], S [auth C], U [auth E], W [auth F]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG	M [auth A], R [auth C], V [auth F]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900004	G, H, I, J, K, L	beta-lactose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.197 (Depositor), 0.196 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.188 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.52	α = 90
b = 193.83	β = 90
c = 108.17	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SHARP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
HKL-2000	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-12-03 
Deposition Author(s): Dessau, M.

Revision History  

• Version 1.0: 2014-12-03
  Type: Initial release
  
• Version 1.1: 2019-07-17
  Changes: Data collection, Derived calculations, Refinement description
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2024-02-28
  Changes: Data collection, Database references, Structure summary